Annual and Seasonal Dissolved Inorganic Nutrient Budgets

Home , Bay mud, Mad River (California)

ANNUAL AND SEASONAL DISSOLVED INORGANIC NUTRIENT BUDGETS

FOR HUMBOLDT BAY WITH IMPLICATIONS FOR WASTEWATER

DISCHARGERS

Charles R. Swanson

A Project Report Presented to

The Faculty of Humboldt State University

In Partial Fulfillment of the Requirements for the Degree

Master of Science in Environmental Systems:

Environmental Resources Engineering

Committee Membership

Dr. Brad Finney, Committee Chair

Dr. Matthew Hurst, Committee Member

Dr. Robert Gearheart, Committee Member

December 2015

ABSTRACT

ANNUAL AND SEASONAL DISSOLVED INORGANIC NUTRIENT BUDGETS FOR HUMBOLDT BAY WITH IMPLICATIONS FOR WASTEWATER DISCHARGERS

Charles R. Swanson

Dissolved inorganic nutrient loading and uptake have been estimated for each of the four major compartments of Humboldt Bay for the two major seasons characterized by ocean upwelling (April through September) and watershed runoff (October through

March). Dissolved inorganic nutrient loading estimations include dissolved inorganic nitrogen (DIN) as ammonium-N, nitrate-N, and nitrite-N, dissolved inorganic phosphorus

(DIP) as phosphate-P, and dissolved inorganic silicon (DSi) as silicate-Si. DIN and DIP uptake estimations include phytoplankton, macroalgae, and eelgrass production, intertidal sediment flux, and denitrification. A water budget including tidal flows, watershed runoff, wastewater discharge, and direct precipitation on the Bay is also included as a means for determining mass inputs from various sources using concentration data.

Humboldt Bay is a nitrogen limited system exhibiting stoichiometric N:P ratios below the 16:1 Redfield ratio. N:P ratios decrease significantly inside Arcata Bay (the inner-most compartment of Humboldt Bay) compared with water near the Bay entrance during the upwelling season, indicating that denitrification is a major contributor to nitrogen removal from the system during these periods. This also suggests that Arcata

Bay is more nitrogen limited than nearshore waters, as denitrification removes N and not ii

P from the system. Annual estimates of denitrification in Humboldt Bay using areal denitrification rates from a nearby tidal estuary indicate that denitrification may be over five-times greater than the total wastewater DIN discharge, 768 Mg N/yr and 149 Mg

N/yr, respectively. Estimates of phytoplankton, macroalgae, and eelgrass production in the Bay are also greater than wastewater DIN discharge loads.

Freshwater DIN and DIP loads to Humboldt Bay are minor in comparison with estimates of nearshore nutrient loading. Average annual DIN and DIP loading to

Humboldt Bay from nearshore waters is approximately 14,363 Mg N/yr and 2,653 Mg

P/yr, respectively, with only 1.7% of the total nearshore load, 239 Mg N/yr and 44 Mg

P/yr, respectively, estimated to be directly loaded to Arcata Bay. DIN inputs to Arcata

Bay from freshwater sources including wastewater and watershed runoff contribute 40

Mg N/yr and 51 Mg N/yr, respectively, or 17% and 21% of the estimated load from nearshore waters, respectively. DIP inputs to Arcata Bay from wastewater and watershed discharges contribute 13 Mg P/yr and 6 Mg P/yr, respectively, or 21% and 10% of the nearshore load, respectively. During the upwelling and runoff seasons, the Arcata wastewater treatment facility (AWTF) DIN discharge to Arcata Bay makes up 5% and

18% of the total load to the Bay, respectively, and 16% and 25% of the DIP load, respectively.

Eutrophication potential in Humboldt Bay increases during the productive upwelling season as biological uptake of DIN and DIP increase by an estimated 250% and 415%, respectively, and nearshore loading increases by 20% and 14%, respectively.

Watershed runoff DIN and DIP loads decrease during the upwelling season by an iii

estimated 74%, and wastewater loads decrease by an estimated 32% and 20%, respectively. Decreased DIN and DIP discharge from wastewater and watershed sources during the productive upwelling season suggest that anthropogenic nutrient impacts to potential eutrophication in Humboldt Bay are minor in comparison to nearshore influences.

ACKNOWLEDGEMENTS

I would like to thank Professor Matt Hurst who introduced me to research, provided years of guidance in the laboratory, secured grant money for our work, and got me interested in Humboldt Bay. I would like to thank the Wiyot Tribe's Natural

Resources Department staff including Stephen Kullmann and Tim Nelson for their years of high quality monitoring and sample collection in Humboldt Bay, and for maintaining the data sonde on Indian Island that continues to provide the best and longest running near-real time dataset in Humboldt Bay. I would like to thank Professor Bob Gearheart for giving me the opportunity to learn from his lifetime of experience at the Arcata Marsh and for providing material support for this project. I would like to thank Professor Brad

Finney for years of support in and out of the classroom as I endlessly over-committed myself. I would like to thank Jeff Anderson, P.E. for his support in providing detailed output from his hydrodynamic model and for taking the time to meet with me over the years to teach my how to use the model software. I would like to thank Kenny Smith for all of his help collecting, processing, and analyzing samples including some very windy days on the Bay. I would like to thank the City of Arcata Environmental Services department, in particular Erik Lust, Mark Andre, Karen Diemer, and Rachel Hernandez, for their support of this project well in advance of any regulatory necessity. I would like to thank Professor Jeff Abel for the use of his autoanalyzer to run all of our nutrient samples. I would like to thank the Humboldt State University Telonicher Marine

Laboratory in Trinidad for the use of their facilities including the autoanalyzer and

fluorometer. I would like to thank the Humboldt State University Sponsored Programs

Foundation for their financial support that helped us pay for laboratory supplies and student labor. I would like to thank the City of Eureka wastewater treatment facility staff for readily providing water quality data and their openness to letting me grab samples and run independent nutrient tests on them. I would like to thank Jennifer Kalt at Humboldt

Baykeeper for providing their citizen monitoring dataset. I would like to extend a special thank you to Juliette Bohn for her unending patience, love, support, and enthusiasm, and most of all for the use of her Zodiac!

TABLE OF CONTENTS

ABSTRACT ...... ii

ACKNOWLEDGEMENTS ...... v

TABLE OF CONTENTS ...... vii

LIST OF TABLES ...... xii

LIST OF FIGURES ...... xvii

LIST OF ABBREVIATIONS ...... xxii

LIST OF UNITS ...... xxiv

INTRODUCTION ...... 1

Geographic Setting ...... 2

Hydrographic Setting ...... 5

Watershed Characteristics ...... 7

Arcata Bay ...... 10

Main Channel ...... 13

Entrance Bay ...... 15

South Bay ...... 17

Oceanographic Setting ...... 18

Ecologic Setting ...... 22

Wastewater ...... 24

REVIEW OF LITERATURE ...... 26

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Nutrient Cycling ...... 27

Nitrogen Cycle ...... 28

Phosphorus Cycle ...... 30

Silicon Cycle ...... 31

Nutrient Sources and Uptake ...... 32

Atmospheric Fixation ...... 33

Phytoplankton Production ...... 33

Eelgrass Production ...... 35

Macroalgae Production ...... 35

Salt Marsh Production ...... 36

Mariculture ...... 37

Sediment Flux ...... 38

Denitrification ...... 42

Humboldt Bay Flushing Times ...... 45

Humboldt Bay Circulation Studies ...... 49

Humboldt Bay Nutrient Studies ...... 54

METHOD ...... 65

Sample Collection ...... 65

Sample Analyses ...... 72

Data Analyses ...... 74

Tidal Volumes ...... 79

Watershed Runoff Volumes ...... 81

Precipitation Volumes ...... 83

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Ocean Nutrient Loads ...... 83

Wastewater Nutrient Loads ...... 84

Watershed Nutrient Loads ...... 85

Phytoplankton Uptake ...... 86

Macroalgae Uptake ...... 88

Eelgrass Uptake ...... 89

Sediment Flux ...... 90

Denitrification ...... 92

RESULTS ...... 94

Upwelling Season Response ...... 95

Runoff Season Response ...... 100

Nitrogen Limitation ...... 108

Eutrophication Level ...... 110

Climatic Anomalies ...... 113

Intertidal Properties ...... 114

Chlorophyll-a ...... 117

Nitrate ...... 120

Silicate ...... 124

Ammonium ...... 127

Phosphate ...... 130

Nutrient Sources ...... 132

Ocean Influx ...... 132

Wastewater Discharge...... 133

Watershed Runoff ...... 140

Sediment Flux ...... 143

Nutrient Uptake ...... 144

Phytoplankton Uptake ...... 144

Macroalgae Uptake ...... 148

Eelgrass Uptake ...... 150

Sediment Flux ...... 151

Denitrification ...... 156

Water Budget ...... 157

Nutrient Budgets ...... 161

Annual DIN Budget ...... 161

Seasonal DIN Budgets ...... 167

Annual Phosphate-P Budget ...... 169

Seasonal Phosphate-P Budgets ...... 171

Annual Silicate-Si Budget ...... 174

Seasonal Silicate-Si Budgets ...... 175

DISCUSSION ...... 178

Seasonal Responses ...... 178

Budget Surpluses ...... 180

Budget Deficits ...... 181

Comparison with Other Systems ...... 182

Historical Changes ...... 185

FUTURE RESEARCH ...... 188

CONCLUSION ...... 189

REFERENCES ...... 190

APPENDIX A - SAMPLE SITE COORDINATES ...... 201

APPENDIX B - WATER QUALITY DATA ...... 202

LIST OF TABLES

Table 1 - Surface area and volume for Humboldt Bay at various tidal data; note these data are from a hydrodynamic model that includes portions of Mad River Slough, Freshwater Slough, and Martin's Slough, so high tide values are slightly greater than listed elsewhere...... 5

Table 2 - Average monthly precipitation for the period of record (12/1/1886-1/20/2015) at Woodley Island in Eureka...... 6

Table 3 - Average daily flow rates for the two major wastewater treatment facilities discharging to Humboldt Bay...... 7

Table 4 - Humboldt Bay sub-watershed surface areas...... 8

Table 5 - Water to watershed surface areas ratios for Pacific coast bays...... 8

Table 6 - Surface area and volume of Arcata Bay at different tidal datums...... 11

Table 7 - Surface area and volume of the Main Channel at different tidal data...... 14

Table 8 - Surface area and volume of Entrance Bay at different tidal data...... 16

Table 9 - Surface area and volume of South Bay at different tidal data...... 18

Table 10 - Tidal data from the NOAA North Spit, Humboldt Bay station...... 19

Table 11 - Phytoplankton assimilation ratios from three independent studies (g/hr/g Chl- a); it should be noted that these values vary significantly, likely due to variations in ambient nutrient concentrations that can influence phytoplankton uptake rates...... 35

Table 12 - Nutrient flux rates for microalgae-covered intertidal sediments in Yaquina Bay, Oregon (mg/m2/hr); negative values denote sediment uptake...... 41

Table 13 - Phosphate and silicate concentration ranges measured near the Bay entrance, in Arcata Bay, and in South Bay...... 55

Table 14 - Phosphate, nitrate, and ammonium concentration ranges (and medians) measured near the Bay entrance and inside Arcata Bay between July 1979 and March 1980...... 58

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Table 15 - Phosphate, nitrate, ammonium, and silicate concentration ranges (and means) measured near the Bay entrance, in Arcata Bay, and in South Bay...... 59

Table 16 - Dry Season phosphate, nitrate, and ammonium concentration ranges (and means) measured throughout Humboldt Bay; note that low and high range values were estimated from plots, whereas means were gathered from tabulated data...... 63

Table 17 - Wet season phosphate, nitrate, and ammonium concentration ranges (and means) measured throughout Humboldt Bay; note that low and high range values were estimated from plots, whereas means were gathered from tabulated data...... 64

Table 18 - Ranges (and medians) of phosphate, nitrate, nitrite, and silicate measured in Humboldt Bay...... 64

Table 19 - Sub-bay and associated watershed surface areas...... 79

Table 20 - Surface area and streamflow characteristics for each stream entering Humboldt Bay and nearby Little River...... 82

Table 21 - Monthly macroalgae production rates measured in Coos Bay, Oregon; % RSD is the percent of the standard deviation relative to the mean...... 88

Table 22 - Average monthly eelgrass production rates measured in Arcata Bay and South Bay...... 90

Table 23 - Monthly light and dark period intertidal sediment flux rates for nitrate and ammonium; values in bold are actual measurements, values in italics are linearly interpolated between measured values (bold)...... 91

Table 24 - Monthly light and dark period intertidal sediment flux rates for phosphate and silicate; values in bold are actual measurements, values in italics are linearly interpolated between measured values (bold)...... 92

Table 25 - Eutrophication classification system based upon maximum annual chlorophyll-a concentrations in an estuary developed by the National Estuarine Eutrophication Assessment (Bricker et al., 2003)...... 111

Table 26 - Eutrophication classification system based upon minimum annual dissolved oxygen concentrations in an estuary developed by the National Estuarine Eutrophication Assessment (Bricker et al., 2003)...... 113

Table 27 - Total annual precipitation at Woodley Island during the sampling period was between 50-84% of the average for the period of record...... 114

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Table 28 - Average annual and seasonal chlorophyll-a and nutrient loading to Humboldt Bay (and standard deviations)...... 133

Table 29 - Nutrient concentration and loading ranges (and means) for the AWTF and EWTF; only one value for nitrate and phosphate were collected for EWTF effluent on August 31, 2015...... 137

Table 30 - AWTF annual and seasonal hydraulic and nutrient loading to Humboldt Bay (and standard deviations)...... 139

Table 31 - EWTF annual and seasonal hydraulic and nutrient loading to Humboldt Bay (and standard deviations); note that only one measurement of nitrate and phosphate were available so the uncertainty reported for these values is attributed completely to the variation in flow rate used to calculate the mass discharge...... 140

Table 32 - Annual watershed hydraulic and nutrient loading to Humboldt Bay (and standard deviations)...... 142

Table 33 - Upwelling season (April-September) watershed hydraulic and nutrient loading to Humboldt Bay (and standard deviations)...... 143

Table 34 - Runoff season (October-March) watershed hydraulic and nutrient loading to Humboldt Bay (and standard deviations) ...... 143

Table 35 - Average annual and seasonal chlorophyll-a concentrations for sub-bay and average volume of each bay...... 145

Table 36 - Annual phytoplankton nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*; note that silicon uptake assumes all phytoplankton are diatoms and represents an upper estimation...... 147

Table 37 - Upwelling season phytoplankton nutrient uptake for Humboldt Bay and sub- bays (and standard deviations)*...... 148

Table 38 - Runoff season phytoplankton nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*...... 148

Table 39 - Annual macroalgae nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*...... 149

Table 40 - Upwelling season macroalgae nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*...... 150

Table 41 - Runoff season macroalgae nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*...... 150 xiv

Table 42 - Annual eelgrass nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*; note that reported eelgrass production only takes place during the upwelling season (April-September) therefore the annual uptake is the upwelling season uptake. 151

Table 43 - Annual sediment nutrient flux for Humboldt Bay and sub-bays (and standard deviations)*; negative flux values indicate uptake by sediments...... 155

Table 44 - Upwelling season sediment nutrient flux for Humboldt Bay and sub-bays (and standard deviations)*; negative flux values indicate uptake by sediments...... 156

Table 45 - Runoff season sediment nutrient flux for Humboldt Bay and sub-bays (and standard deviations)*; negative flux values indicate uptake by sediments...... 156

Table 46 - Annual denitrification in Humboldt Bay and sub-bays (and standard deviations)...... 157

Table 47 - Annual water budget for Humboldt Bay (Mm3/yr); the Entrance Bay may be influenced by Eel River water in the winter when nearshore currents flow northward though it does not receive any direct river inputs...... 159

Table 48 - Upwelling season water budget for Humboldt Bay (Mm3)...... 160

Table 49 - Runoff season water budget for Humboldt Bay (Mm3)...... 160

Table 50 - Annual DIN budget including loading and uptake for Humboldt Bay and sub- bays (Mg N/yr); negative values denote uptake or removal from the system...... 165

Table 51 - Bay entrance DIN export for 12 monthly samples illustrates the potential for advective export of nutrients from Humboldt Bay as an additional sink to account for the large net surplus of nutrients in the budget (total net export in this example is 16,550 Mg N/yr)...... 166

Table 52 - Annual volumetric DIN loading and uptake rates for Humboldt Bay and sub- bays...... 166

Table 53 - Upwelling season DIN loading and uptake for Humboldt Bay and sub-bays (Mg N)...... 168

Table 54 - Runoff season DIN loading and uptake for Humboldt Bay and sub-bays (Mg N)...... 169

Table 55 - Annual phosphate-P loading and uptake for Humboldt Bay and sub-bays (Mg P/yr)...... 171

Table 56 - Upwelling season phosphate-P loading and uptake for Humboldt Bay and sub- bays (Mg P)...... 173

Table 57 - Runoff season phosphate-P loading and uptake for Humboldt Bay and sub- bays (Mg P)...... 174

Table 58 - Annual silicate loading and uptake in Humboldt Bay and sub-bays (Mg Si/yr); phytoplankton uptake assumes all phytoplankton in Humboldt Bay are diatoms, making this an upper estimate of possible phytoplankton silicate uptake...... 175

Table 59 - Upwelling season silicate-Si loading and uptake for Humboldt Bay and sub- bays (Mg Si); phytoplankton uptake assumes all phytoplankton in Humboldt Bay are diatoms, making this an upper estimate of possible phytoplankton silicate-Si uptake. .. 176

Table 60 - Runoff season silicate-Si loading and uptake for Humboldt Bay and sub-bays (Mg Si); phytoplankton uptake assumes all phytoplankton in Humboldt Bay are diatoms, making this an upper estimate of possible phytoplankton silicate-Si uptake...... 177

Table 61 - Comparison of physical properties and biological uptake in Humboldt Bay and Tomales Bay...... 183

Table 62 - Comparison of nitrate and ammonium concentrations in Humboldt Bay and Tomales Bay; outer bay refers to areas near the bay entrance more highly influenced by nearshore conditions, and inner bay refers to areas more isolated from nearshore influences...... 184

Table 63 - Comparison of nitrate and ammonium concentrations in Humboldt Bay and eutrophic Upper Newport Bay in Southern California; note that creek nitrate and ammonium concentrations in Humboldt Bay are the same for both seasons due to insufficient data; tidal channel refers to areas inside the bay, and creek refers to watershed and creek runoff...... 185

Table 64 - Comparison of historic nutrient concentrations measured in Humboldt Bay between 1962-2015; IB = Inner Bay (i.e. Arcata Bay or South Bay), OB = Outer Bay (i.e. near Bay Entrance), US = Upwelling Season, RS = Runoff Season, ND = no data...... 187

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LIST OF FIGURES

Figure 1 - Humboldt Bay (40.8° N, 124.2° W) is located in northern California approximately 80 miles south of the California-Oregon Border (Google Earth (1), 2013)...... 3

Figure 2 - Humboldt Bay consists of four distinctive compartments, and is adjoined by two cities, Arcata and Eureka; note: image depicts Humboldt Bay at low tide (NAIP, 2014)...... 4

Figure 3 - Humboldt Bay watershed delineation (WBD, 2015); note, alterations have been made to the Watershed Boundary Database polygons to more precisely represent the contributing watersheds of Humboldt Bay based on the location of tide gates and sample points...... 9

Figure 4 - Aerial imagery of Arcata Bay indicating major circulation channels and freshwater input locations (ortho-imagery: NAIP 2014)...... 10

Figure 5 - Aerial imagery of the Main Channel indicating the location of major flow channels and freshwater inputs (ortho-imagery: NAIP 2014)...... 14

Figure 6 - Aerial imagery of Entrance Bay indicating the locations of major landmarks, flow channels, and freshwater inputs (ortho-imagery: NAIP, 2014)...... 16

Figure 7 - Aerial imagery of South Bay indicating the locations of major flow channels, landmarks, and freshwater inputs (ortho-imagery: NAIP 2014)...... 17

Figure 8 - Average monthly upwelling indices for two locations off the northern California coast (PFEL, 2015); note: Humboldt Bay is located at approximately 40.8 degrees north latitude...... 20

Figure 9 - Location of three calculated upwelling indices; 42N is near the California- Oregon border, 39N is approximately west of Ukiah, California, and 33N is near San Diego, California (Google Earth (2), 2013)...... 22

Figure 10 - Average monthly precipitation and upwelling represent the two distinctive seasons in Humboldt Bay, October-March and April-September (upwelling data: PFEL 2015, precipitation data: WRCC 2015)...... 24

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Figure 11 - Major nutrient sources, types of biological uptake, and sinks for Humboldt Bay...... 27

Figure 12 - Major processes of the nitrogen cycle in estuaries and coastal waters: (i) nitrogen fixation, (ii) ammonium assimilation, (iii) nitrification, (iv) assimilatory nitrate reduction, (v) ammonification or mineralization, (vi) ammonium oxidation, (vii) denitrification, and (viii) dissolved organic nitrogen assimilation (Bianchi, 2013)...... 30

Figure 13 - Three short-term tracer dye studies conducted in Arcata Bay to determine the extent of potential treated wastewater contamination of oyster beds (adapted from Klamt, 1979)...... 51

Figure 14 - Sample site map and distances from the mouth of Humboldt Bay...... 68

Figure 15 - Professor Hurst's sample site map and distances from the mouth of Humboldt Bay...... 69

Figure 16 - Wiyot Tribe's sample site map and distances from the mouth of Humboldt Bay...... 70

Figure 17 - Wastewater treatment facility outfall map and distances from the mouth of the Bay...... 71

Figure 18 - Sub-bay boundary map...... 78

Figure 19 - Humboldt Bay EFDC model outline and sub-bay flux line map (Anderson, 2015)...... 80

Figure 20 - Example intra-bay flow rates for one tide cycle on January 1, 2012 from EFDC hydrodynamic model (Anderson, 2015); positive values denote flood tide and negative values denote ebb tide...... 81

Figure 21 - Average upwelling season nutrient concentrations in each sub-bay between 2007 and 2015 (Hurst, 2009; Wiyot Tribe Natural Resources Department, 2015; this study)...... 97

Figure 22 - Average monthly high tide nitrate concentrations at the Bay entrance and upwelling indices for water years 2008, 2009, 2013, and 2014 (Wiyot Tribe Natural Resources Department, 2015; this study; PFEL, 2015)...... 98

Figure 23 - Average monthly high tide silicate concentrations at the Bay entrance and upwelling indices for water years 2008, 2009, 2013, and 2014 (Wiyot Tribe Natural Resources Department, 2015; this study; PFEL, 2015)...... 98

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Figure 24 - Average monthly high tide ammonium concentrations at the Bay entrance and upwelling indices for water years 2013, and 2014 (Wiyot Tribe Natural Resources Department, 2015; this study; PFEL, 2015)...... 99

Figure 25 - Average monthly high tide phosphate concentrations at the Bay entrance and Bakun upwelling indices (Wiyot Tribe Natural Resources Department, 2015; this study; PFEL, 2015)...... 99

Figure 26 - Average seasonal nitrate concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 101

Figure 27 - Average monthly nitrate concentrations at Mad River Slough and total monthly precipitation at Woodley Island (WRCC, 2015) and for water years 2008, 2009, 2013, and 2014 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 101

Figure 28 - Average seasonal ammonium concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 103

Figure 29 - Average monthly ammonium concentrations at Mad River Slough and total monthly precipitation at Woodley Island (WRCC, 2015) for water years 2008, 2009, 2013, and 2014 (Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 103

Figure 30 - Average seasonal silicate concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 105

Figure 31 - Average monthly silicate concentrations at Mad River Slough and total monthly precipitation at Woodley Island (WRCC, 2015) for water years 2008, 2013, and 2014 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 105

Figure 32 - Average seasonal phosphate concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 107

Figure 33 - Average monthly phosphate concentrations at Mad River Slough and total monthly precipitation at Woodley Island (WRCC, 2015) for water years 2008, 2009, 2013, and 2014 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 107

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Figure 34 - Stoichiometric nitrogen to phosphorus (N:P) ratios in Arcata Bay and Entrance Bay during calendar year 2014; the "Redfield ratio" of 16:1 represents the stoichiometric N:P ratio in phytoplankton biomass...... 109

Figure 35 - Nitrate was typically the major dissolved inorganic nitrogen species in coastal waters entering the Bay between October 2012 and February 2015 (Wiyot Tribe Natural Resources Department, 2015; this study)...... 109

Figure 36 - Average maximum annual upwelling and runoff season chlorophyll-a concentrations in Humboldt Bay measured during WY 2013 and WY 2014 (Hurst 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 111

Figure 37 - Minimum dissolved oxygen concentrations in Humboldt Bay measured during WY 2013 and WY 2014 (Hurst 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study)...... 112

Figure 38 - Total monthly direct normal solar insolation for water years 2008, 2009, 2013, and 2014 (SoRMS, 2015)...... 114

Figure 39 - Longitudinal and intertidal temperature gradients are greatest during the summer as water is heated over the shallow intertidal mud flats at low tide...... 116

Figure 40 - Longitudinal and intertidal salinity gradients are greatest during the runoff season as freshwater runoff dilutes Arcata Bay...... 116

Figure 41 - Chlorophyll-a concentrations at Indian Island peak at high tide indicating phytoplankton populations inside the Bay may originate from closer to the ocean or that predation inside the Bay reduces concentrations (Wiyot Tribe Natural Resources Department, 2015)...... 118

Figure 42 - High and low tide chlorophyll-a concentrations along a longitudinal transect from the Bay entrance to Arcata Bay...... 119

Figure 43 - High and low tide nitrate concentrations along a longitudinal transect from the Bay entrance to Arcata Bay...... 123

Figure 44 - High and low tide silicate concentrations along a longitudinal transect from the Bay entrance to Arcata Bay...... 126

Figure 45 - High and low tide ammonium concentrations along a longitudinal transect from the Bay entrance to Arcata Bay...... 129

Figure 46 - High and low tide phosphate concentrations along a longitudinal transect from the Bay entrance to Arcata Bay...... 131

Figure 47 - AWTF effluent ammonium, nitrate, and phosphate concentrations between April 2011 and April 2015 (City of Arcata, 2015); note wastewater concentrations are typically reported as mg/L...... 134

Figure 48 - AWTF daily discharge flow rates between April 2011 and April 2015 indicate significant seasonal fluctuation of discharge flow rates with peaks occurring in the winter time due to increased inflow and direct precipitation on the 90 acre facility (City of Arcata, 2015); note wastewater flow rates are typically reported as million gallons per day (MGD)...... 135

Figure 49 - AWTF effluent ammonium, nitrate, and phosphate mass loads between April 2011 and April 2015 (City of Arcata, 2015); note Mg refers to million grams, equivalent to one metric ton...... 135

Figure 50 - EWTF ammonium discharge concentration and mass load indicate seasonal peaks may occur during the summer, and that there is little effect of dilution (City of Eureka, 2015); note wastewater flow rates are typically reported as million gallons per day (MGD)...... 136

Figure 51 - Average monthly intertidal sediment nutrient fluxes using flux rates from Sin et al. (2007) and the intertidal surface area of Humboldt Bay...... 155

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LIST OF ABBREVIATIONS

AWTF - Arcata wastewater treatment facility BOD - Biochemical oxygen demand C - Carbon Chl-a - Chlorophyll-a DIN - Dissolved inorganic nitrogen DIP - Dissolved inorganic phosphorus DO - Dissolved oxygen DOC - Dissolved organic carbon DON - Dissolved organic nitrogen DSi - Dissolved inorganic silicon EWTF - Eureka wastewater treatment facility max - maximum MHW - Mean high water elevation MHHW - Mean higher high water elevation min - minimum MLW - Mean low water elevation MLLW - Mean lower low water elevation mo - month MSL - Mean sea level elevation N - Nitrogen NA - Not applicable NAVD88 - National vertical datum of 1988 ND - No data NEP - Net ecosystem production P - Phosphorus xxii

Si - Silicon TSS - Total suspended solids UTM10 - Universal transverse mercator: zone 10 (geospatial projection) WWTF - Wastewater treatment facility

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LIST OF UNITS ac - acre °C - degrees Celsius °F - degrees Fahrenheit ft - feet g - grams hr - hours in - inches kg - kilograms kWh - kilowatt-hours L - liters m - meters m3 - cubic meters Mg - megagrams MGD - million gallons per day mg/L - milligrams per liter mi - miles mi2 - square miles mM - milimolar Mm2 - million square meters Mm3 - million cubic meters n - number of samples NTU - nephelometric turbidity units ppt - parts per thousand s - seconds µg/L - micrograms per liter xxiv

µm - micrometer µM - micromolar

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INTRODUCTION

Humboldt Bay is a highly productive ecosystem supporting some of the largest eelgrass beds on the Pacific Coast (CDFG, 2010), and is the most productive oyster mariculture site in California (H.T. Harvey & Associates, 2015). Every aspect of biological activity in the Bay relies on the supply of nutrients to support a productive food web; however, an excess of nutrients can result in overproduction, or eutrophication.

Eutrophication can result in a loss of submerged aquatic vegetation, reduced wildlife habitat, poor water quality, and potentially toxic algae blooms (Bricker et al., 2007). The objective of this study is to provide a basis for comparison between wastewater nutrient discharges and other major sources and biological uptake in Humboldt Bay to aide decision makers in establishing management practices that support and protect all of the beneficial uses of the Bay.

North Humboldt Bay (Arcata Bay) is of particular interest because it contains nearly all of the oyster culture in the Bay (H.T. Harvey & Associates, 2015), approximately 60% of the eelgrass beds (Schlosser and Eicher, 2012), receives effluent from the Arcata wastewater treatment facility (AWTF), and experiences limited tidal flushing due to the morphology of the Bay (Anderson, 2010; Pequegnat and Butler, 1982;

Costa, 1982). All of these factors exhibit seasonal variation creating a highly complex and dynamic system. There are currently two proposals to increase oyster mariculture in

Arcata Bay by up to six times current levels of production (H.T. Harvey & Associates,

2015; Coast Seafoods Company, 2015), and the AWTF is undergoing retrofits to improve treatment and effluent quality.

Few studies have assessed nutrient levels in Humboldt Bay and none have characterized the relative magnitudes of sources and types of biological uptake. This nutrient budget combines multiple datasets spanning multiple years to quantify major dissolved inorganic nutrient sources and uptake, characterize seasonal shifts in nutrient uptake and supply to the Bay, and estimate the contribution of major processes involved in nutrient uptake to the overall budget.

Geographic Setting

Humboldt Bay is located approximately 80 miles south of the California-Oregon border (Figure 1) and is the second largest coastal embayment in California next to San

Francisco Bay. Humboldt Bay is adjoined by two cities, Arcata and Eureka (Figure 2).

Arcata borders Humboldt Bay to the North with a population of approximately 17,700, and Eureka borders Humboldt Bay to the East with a population of approximately 27,000

(US Census Bureau, 2014).

Humboldt Bay is made up of two large shallow bays, Arcata Bay and South Bay, a deeper Entrance Bay, and a deep Main Channel connecting Arcata Bay to the Entrance

Bay (Figure 2). Entrance Bay and the Main Channel are dredged and maintained for navigation of large industrial ships, while Arcata Bay and South Bay contain extensive intertidal mud flats and subtidal eelgrass beds providing important habitat and creating unique hydrodynamic characteristics.

Figure 1 - Humboldt Bay (40.8° N, 124.2° W) is located in northern California approximately 80 miles south of the California-Oregon Border (Google Earth (1), 2013).

Figure 2 - Humboldt Bay consists of four distinctive compartments, and is adjoined by two cities, Arcata and Eureka; note: image depicts Humboldt Bay at low tide (NAIP, 2014).

Hydrographic Setting

Humboldt Bay can change in volume by up to 54% during one tide cycle, creating a tidal prism of approximately 114 Mm3 (Table 1). The surface area of the Bay between mean higher high water (MHHW) and mean lower low water (MLLW) tide elevations can change by up to 56% exposing up to 15 mi2 of intertidal mud flats (Anderson, 2015).

Surface Area1 Volume1 Tidal Datum (mi2) (Mm3) MLLW 11.8 97.7 MLW 15.8 111.0 MSL 23.6 148.1 MHW 26.5 199.3 MHHW 26.7 211.6 1Anderson (2015)

Humboldt Bay has been characterized as a protected embayment dominated by subtidal and deep water habitat where the mouth remains open to tidal exchange continuously (Sutula et al., 2007). Estuaries, on the other hand, are typically river- dominated with strong mixing, significant salinity gradients due to freshwater inputs, and stronger ebb tides (Sutula et al., 2007). Measureable dilution can occur in Arcata Bay and South Bay during and after rainfall events, however, this behavior is episodic and temporary (Gast and Skeesick, 1964). During the wet winter season, horizontal stratification occurs with respect to salinity resulting from increased freshwater runoff,

6 and during the dry summer season, horizontal stratification occurs with respect to temperature resulting from warming of water in South Bay and Arcata Bay (Gast and

Skeesick, 1964).

Humboldt Bay lies in a temperate zone receiving approximately 40 inches of rain per year with an average annual air temperature of 53°F (Table 2). Two wastewater treatment facilities discharge into Humboldt Bay contributing an average combined daily flow of approximately 0.030 Mm3/d (7.8 MGD) (Table 3). The public water supply for the region is taken from the Mad River, adjacent to the Humboldt Bay watershed to the

North (the Mad River does not flow into Humboldt Bay).

Table 2 - Average monthly precipitation for the period of record (12/1/1886-1/20/2015) at Woodley Island in Eureka.

Average Average Month Precipitation1 (in.) Temperature1 (°F) January 6.72 48 February 5.31 49 March 5.45 49 April 3.09 50 May 1.67 53 June 0.68 56 July 0.15 57 August 0.32 58 September 0.73 57 October 2.67 55 November 5.61 51 December 7.03 48 Annual 39.45 53 1WRCC (2015)

Table 3 - Average daily flow rates for the two major wastewater treatment facilities discharging to Humboldt Bay.

Month AWTF1 (MGD) EWTF2 (MGD) Total (MGD) January 2.61 5.36 7.97 February 2.82 4.41 7.23 March 3.21 4.53 7.74 April 2.73 4.26 6.99 May 1.74 3.52 5.26 June 1.32 3.42 4.74 July 1.12 3.28 4.40 August 1.21 3.24 4.45 September 1.37 3.32 4.69 October 1.91 3.19 5.10 November 2.24 3.11 5.35 December 2.97 3.35 6.32 Average 2.10 3.75 5.85 1City of Arcata (2015); 2City of Eureka (2015)

Watershed Characteristics

The total surface area of the Humboldt Bay watershed including the Bay is approximately 217 mi2, of which the Bay comprises approximately 27 mi2 (Table 4). The four largest surface water inputs to the Bay that make up approximately 90% of the watershed surface area include Freshwater Creek that enters the Bay north of Eureka, the

Elk River that enters the Bay south of Eureka near the Bay entrance, Jacoby Creek that enters the east side of Arcata Bay, and Little Salmon Creek that enters the southeast side of South Bay (Figure 3). The other four minor freshwater inputs to the Bay all enter

Arcata Bay. Humboldt Bay has a relatively small contributing watershed with no major

8 river inputs compared to other bays and estuaries on the Pacific coast (Table 5). The Bay is also adjoined by approximately 1.41 mi2 of intertidal salt marsh, though this is only approximately 10% of the historic salt marshes that once existed due to diking for agricultural use (Schlosser and Eicher, 2012).

Table 4 - Humboldt Bay sub-watershed surface areas.

Sub-watershed Surface Area1 (mi2) Mad River Slough 8.36 Janes Creek/McDaniel's Slough 4.79 Jolly Giant Creek/Butcher's Slough 1.80 Washington/Rocky Gulches 2.90 Jacoby Creek/Gannon Slough 20.18 Freshwater Creek/ Freshwater Slough and Fay Slough 56.72 Elk River/Martin Slough 55.96 Little Salmon Creek/Hookton Slough 18.47 Rural and urban landscapes 20.08 Salt marshes (Schlosser and Eicher 2012) 1.41 Humboldt Bay (MHHW, Anderson 2015) 26.74 1WBD (2015)

Table 5 - Water to watershed surface areas ratios for Pacific coast bays.

Bay Surface Watershed Surface Bay : Watershed Bay Area (mi2) Area (mi2) Surface Area Ratio (%) Humboldt 26 235 11% San Francisco1 1,600 73,400 2% San Diego2 16.5 415 4% Coos3 17.1 605 3% 1USEPA (2015); 2City of San Diego (2013); 3NAC (2004)

Arcata Bay

Arcata Bay is the northern-most unit of Humboldt Bay, and is isolated from the ocean by the Main Channel and the Entrance Bay. Mad River Slough adjoins the Bay to the northwest (Figure 4) draining an area of salt marshes and agricultural lands known as the Arcata Bottoms. The Mad River Slough Channel drains the western one-third of

Arcata Bay along with all of Mad River Slough. The volume of Arcata Bay can change by up to 57.3 Mm3 during a single tide cycle, 78% of the MHHW volume (Table 6), and the surface area of Arcata Bay can decrease by up to 67% in a single tide cycle exposing up to 9.6 mi2 of intertidal mud flats (Anderson, 2015).

Figure 4 - Aerial imagery of Arcata Bay indicating major circulation channels and freshwater input locations (ortho-imagery: NAIP 2014).

Table 6 - Surface area and volume of Arcata Bay at different tidal datums.

Tidal Datum Surface Area1 (mi2) Volume1 (Mm3) MLLW 4.79 16.36 MLW 6.65 21.70 MSL 12.06 38.53 MHW 14.28 66.94 MHHW 14.42 73.61 1Anderson (2015)

McDaniel's Slough adjoins the Bay to the north and is where Jane's Creek empties into the Bay (Figure 4). Jane's Creek drains a small watershed including low forested hills to the north of Arcata, agricultural land adjoining the City including part of the

Arcata Bottoms, and part of the City of Arcata. McDaniel's Slough is the site of current salt marsh restoration efforts and the future site of the AWTF discharge.

Butcher's Slough is a small salt marsh located near the current outfall of the

AWTF (Figure 4) and receives freshwater from Jolly Giant Creek. Jolly Giant Creek drains a small watershed including low forested hills above Arcata and part of the City as well.

Gannon Slough is the site where Jacoby Creek enters Arcata Bay and includes interspersed tidal salt marshes and stock grazing lands (Figure 4). Jacoby Creek is the largest watershed emptying directly into Arcata Bay and includes forested hills, rural landscapes, and agricultural lands. Freshwater Creek to the south is larger but does not empty directly into Arcata Bay.

Rocky Gulch and Washington Gulch combine freshwater streams from small rural and forested hills in a small salt marsh on the west side of Arcata Bay (Figure 4). The small salt marsh is surrounded by diked agricultural land and enters the Bay near the

Bayside cutoff on US Highway 101.

Freshwater Slough is located on the southeast side of Arcata Bay and is where

Freshwater Creek empties into the Bay (Figure 4). The Freshwater Creek watershed

(including Freshwater Slough, Fay Slough, and Ryan Creek), is the largest sub-watershed of Humboldt Bay draining a large area of low-lying agricultural lands, rural landscapes, and surrounding forested hills. At low and ebbing tides Freshwater Slough drains into the Eureka Channel that joins with the Indian/Woodley Channel before reaching the Main

Channel without mixing with the main flow from Arcata Bay in the Samoa Channel, being separated by Woodley Island and Indian Island (Figure 4). During high and flood tides, the tidal prism may penetrate far into Freshwater Slough preventing discharge into the Bay; only waters that have previously drained into Eureka Channel during the ebb tide may potentially be pushed into the eastern side of Arcata Bay. The amount of mixing between Freshwater Slough waters, the Main Channel, and Arcata Bay may be dependent on the elevations of each tide cycle, discharge flow rate from Freshwater

Slough, and wind speed and direction. These factors combine to reduce the direct influence of Freshwater Slough discharge on Arcata Bay (Klamt, 1979).

Main Channel

The Main Channel of Humboldt Bay connects Arcata Bay to the Entrance Bay and is isolated from the ocean by the Entrance Bay. Elk River is the second largest sub- watershed of Humboldt Bay (WBD, 2015) and empties into the Main Channel south of

Eureka near the EWTF outfall (Figure 5). The Samoa Channel, Indian/Woodley

Channel, and Eureka Channel all converge at the north end of the Main Channel to drain

Arcata Bay and Freshwater Slough. The Main Channel is deeper than Arcata Bay and

South Bay due to dredging for ship navigation to industrial ports on either side of the

Channel (HBHRCD, 2007). Between MHHW and MLLW the tidal prism for the Main

Channel is approximately 11.2 Mm3 (Table 7). Enough volume exists in the Main

Channel at MLLW to contain over half of the maximum tidal prism from Arcata Bay, and enough volume at MHHW to contain more than twice the maximum tidal prism from

Entrance Bay (Anderson, 2015). The surface area of the Main Channel does not change significantly during tidal flux due to the steep side of the channel.

Figure 5 - Aerial imagery of the Main Channel indicating the location of major flow channels and freshwater inputs (ortho-imagery: NAIP 2014).

Table 7 - Surface area and volume of the Main Channel at different tidal data.

Tidal Datum Surface Area1 (mi2) Volume1 (Mm3) MLLW 1.84 30.08 MLW 1.88 32.11 MSL 2.10 35.92 MHW 2.22 40.01 MHHW 2.29 41.24 1Anderson (2015)

Entrance Bay

Entrance Bay is the point of convergence for the ocean, South Bay, and Main

Channel (Figure 6). There are no freshwater inputs flow into Entrance Bay, though the

EWTF outfall is near the northern end of the Bay. The Entrance Bay has enough volume at MLLW to hold 100% of the maximum tidal prisms from South Bay and the Main

Channel combined. The surface area of the Bay varies by approximately 5% between

MLLW and MHHW due to relatively steep sides (Table 8). The entrance channel to the

Bay is deeply dredged to allow industrial ship navigation (HBHRCD, 2007).

Waters of the Entrance Bay are highly transient, acting as a mixing zone for coastal water, Arcata Bay water, and South Bay water (Pequegnat and Butler, 1981).

Entrance Bay water assumes characteristics of North and South Bay waters at ebb tides and of coastal waters at high tides. Nearshore currents flowing northward during the winter runoff season bring fresh water from the Eel River eight miles to the south into the

Bay during flood tides (Barnhart et al., 1992). Nearshore currents flowing southward during the summer may bring water from the Mad River 15 miles to the north into

Humboldt Bay during flood tides.

Figure 6 - Aerial imagery of Entrance Bay indicating the locations of major landmarks, flow channels, and freshwater inputs (ortho-imagery: NAIP, 2014).

Table 8 - Surface area and volume of Entrance Bay at different tidal data.

Tidal Datum Surface Area1 (mi2) Volume1 (Mm3) MLLW 2.96 40.36 MLW 2.97 42.95 MSL 3.10 49.15 MHW 3.11 54.56 MHHW 3.12 56.37 1Anderson (2015)

South Bay

South Bay is isolated from the ocean by the Entrance Bay (Figure 7) and is volumetrically the smallest unit in Humboldt Bay (Anderson, 2015). The surface area of

South Bay can change by up to 68% between MHHW and MLLW exposing up to 4.7 mi2 of intertidal mud flats (Table 9). Little Salmon Creek empties into Hookton Slough on the southeast side of South Bay and is the fourth largest sub-watershed of Humboldt Bay.

Two main channels drain South Bay; Southport Channel drains the western half and

Hookton Channel empties the eastern half.

Figure 7 - Aerial imagery of South Bay indicating the locations of major flow channels, landmarks, and freshwater inputs (ortho-imagery: NAIP 2014).

Table 9 - Surface area and volume of South Bay at different tidal data.

Tidal Datum Surface Area1 (mi2) Volume1 (Mm3) MLLW 2.25 10.91 MLW 4.34 14.24 MSL 6.38 24.52 MHW 6.91 37.74 MHHW 6.91 40.42 1Anderson (2015)

Oceanographic Setting

The tidal prism of Humboldt Bay can be up to 54% of the MHHW volume; however this volume of water may not be completely replaced by new ocean water due to limited mixing in the nearshore environment (Barnhart et al., 1992). Ebb tide water from

Humboldt Bay may differ from nearshore waters with respect to temperature and salinity creating stratification due to differences in water density that limit mixing in the nearshore environment (Gast and Skeesick, 1964). Speed and direction of nearshore currents also play a role in the exchange of Bay and ocean waters; ebb tide water from the Bay may simply flow back into the Bay if nearshore currents are not sufficient to advect the volume away from the mouth of the Bay before the flood tide begins.

Humboldt Bay waters also differ in composition from nearshore water with respect to trace metals and nutrients due to upwelling of deep ocean waters (Martin and Hurst,

2008). Each compartment in Humboldt Bay (Entrance Bay, Arcata Bay, Main Channel, and South Bay) may also experience limited mixing with adjacent compartments during tidal exchange due to differences in the physical makeup of each water body.

The mean tidal range at the entrance to Humboldt Bay is 4.89 ft, with a great diurnal range (MHHW to MLLW) of 6.85 ft (Table 10). Tides in Arcata Bay generally exhibit an increase in amplitude and a lag in phase from those observed at the mouth of the Bay (Costa, 1982) indicating that there is some restriction to tidal flow between the two. Tides at Humboldt Bay typically exhibit diurnal inequality with a high-high, high- low, low-high, and low-low tide occurring daily (Barnhart et al., 1992).

Table 10 - Tidal data from the NOAA North Spit, Humboldt Bay station.

Water Surface Elevation1 Tidal Datum (ft, NAVD88) MLLW -0.33 MLW 0.92 MSL 3.37 MHW 5.81 MHHW 6.52 1NGS (2015)

One of the main driving factors in northern California coastal food web productivity is upwelling of deep, nutrient-rich ocean waters. This process occurs when sustained along-shore winds blow southward for one to two weeks, creating currents that transport nutrient-rich subsurface waters to the photic zone (Peterson et al., 2012). This typically occurs during the spring and summer in northern California, creating a season of high productivity in coastal waters (Figure 8). Nitrate, phosphate, and silicate concentrations of 34 µM (Sigleo et al., 2005), 2 µM (van Geen et al., 2000), and 42 µM

(van Geen et al., 2000), respectively, have been measured in upwelled waters off of the

Oregon coast. Lower nutrient concentrations (5-20 µM nitrate, 0.1-1.8 µM phosphate, and 1-33 µM silicate) were measured in warmer surface waters attributed to non- upwelled ocean water.

Figure 8 - Average monthly upwelling indices for two locations off the northern California coast (PFEL, 2015); note: Humboldt Bay is located at approximately 40.8 degrees north latitude.

The Bakun upwelling index describes the volumetric transport of surface water offshore based upon the Ekman theory of mass transport due to wind stress (Schwing et al., 1996). The Bakun index assumes that the amount of surface water transported offshore is directly replaced by deeper upwelled water. The Ekman theory states that in the northern Hemisphere, transport will occur 90 degrees to the right of the direction of wind stress, i.e. southward winds will result in transport of surface waters in the offshore direction (Sverdrup et al., 1942). The opposite phenomenon is termed downwelling and

21 results in transport of surface waters into the deeper ocean. Downwelling can act as a significant sink for nutrients leaving the Bay during the runoff season.

Humboldt Bay lies at approximately 40.8 degrees north latitude (40.8N), in between the two locations where upwelling is calculated by PFEL, 39N and 42N (Figure

9). The highest upwelling on the west coast occurs at approximately 33 degrees north latitude and decreases going north (Schwing et al., 1996). As continental shelf currents that influence coastal conditions reverse direction throughout the year due to changes in wind patterns (Schwartzlose and Reid, 1972), the latitude-specific upwelling index representing conditions at Humboldt Bay may change. As the California Current flows southward during the spring and summer, the upwelling index at 42N may produce a more accurate depiction of upwelling events offshore from Humboldt Bay. During the winter when the Davidson current flows northward along the coast, the upwelling index at 39N may be more reliable for predicting upwelling events near Humboldt Bay. For simplification, the upwelling index at 42N is used in this analysis because this location is more representative of conditions near Humboldt Bay during the upwelling season.

Ecologic Setting

Humboldt Bay is made up of four morphologically distinct water bodies that experience a limited amount of mixing between tide cycles, periodically resulting in distinct water quality and habitat characteristics (Pequegnat and Butler, 1982). The limited exchange between each unit with nearshore waters has been the focus of multiple

23 oceanographic studies attempting to determine the extent to which nutrients and phytoplankton influence water quality inside the Bay.

Arcata Bay is isolated from nearshore waters by the Main Channel and the

Entrance Bay, and has been of particular concern with respect to water quality due to the amount of oyster farming conducted there and potential threats to human health from consumption of contaminated shellfish (Shellfish Protection Act of 1993, 1993).

Isolation from nearshore waters contributes to distinct water quality characteristics particularly during the summer when surface water inflows are low and water temperatures in the Bay increase above nearshore water temperatures (Gast and Skeesick,

1964). During initial precipitation events in the fall and winter, surface water runoff introduces pathogenic bacteria to Arcata Bay often resulting in a temporary halt to oyster harvesting (Geist, 2003). Human health issues surrounding oyster production in Arcata

Bay is one reason leading to the requirement that the AWTF disinfect its treated effluent prior to discharge into the Bay.

In general, upwelling and runoff events can occur at any time throughout the year and the transition from one season to another may vary (Garcia-Reyes and Largier,

2012). However, two distinct seasons can be observed in Humboldt Bay with respect to nutrient supply, the upwelling-influenced season of April through September, and the runoff-influenced season of October through March (Figure 10). During the upwelling season, nutrients are introduced into Humboldt Bay from ocean upwelling, while during the runoff season, upwelling influences decrease and runoff from the surrounding watershed increases (Gast and Skeesick, 1964).

Wastewater

Currently two wastewater treatment facilities discharge into Humboldt Bay, the

Arcata wastewater treatment facility (AWTF) and the Eureka wastewater treatment facility (EWTF), also known as the Elk River wastewater treatment facility. The AWTF continuously discharges into the northern end of Arcata Bay and the EWTF discharges near the entrance to Humboldt Bay on outgoing tides such that they are currently permitted as an ocean discharge. While nutrients are not currently regulated for wastewater discharged to Humboldt Bay, the AWTF has been monitoring nutrients since

2009 to better understand the behavior of their system with respect to nutrient dynamics

(Swanson, 2013).

Wastewater nutrient discharges may be a significant source of nitrogen and phosphorus to Humboldt Bay (Pequegnat and Butler, 1981; Barnhart et al., 1992).

Barnhart et al. (1992) refer to work conducted by Pequegnat and Butler (1981) indicating that 20-50% of the fixed nitrogen in Arcata Bay during the low runoff summer season in

1979 may have been from Eureka's treated wastewater. Many improvements have been made to Eureka's wastewater treatment system as well as Arcata's system between then and now; Pequegnat and Butler (1981) indicate that reduction of wastewater nitrogen may have a significant impact on the ecology of Bay by reducing its overall productivity due to nitrogen limited production.

Wastewater treatment typically emphasizes the removal of biochemical oxygen demand (BOD) and total suspended solids (TSS). BOD and TSS are broad water quality characteristics that encompass a number of physical and biological processes directly influenced by nutrient dynamics. The AWTF uses a constructed wetland treatment system that exhibits natural seasonal variability in nutrient discharge levels due to changes in biological activity. The EWTF uses a more conventional system that may not vary as much seasonally with respect to nutrient removal. Both systems experience increased flow rates following rainfall events due to infiltration and inflow to their systems; increased flow rates can result in increased discharge loads to the Bay.

REVIEW OF LITERATURE

There are many nutrient sources and types of biological uptake in estuarine environments governed by physical, chemical, and biological transport and cycling

(Figure 11). Physical processes include advection of water containing dissolved and particulate matter from stream runoff and ocean tides, and anthropogenic point source discharges of treated wastewater. Chemical processes include diffusion, adsorption of dissolved ions onto particles, and oxidation and reduction reactions influenced by temperature, pH, and relative concentration of chemical species in equilibrium. Major biological processes in an estuarine ecosystem can generally be broken down into autotrophic and heterotrophic (Hagy and Kemp, 2013). Autotrophic organisms utilize inorganic nutrients to synthesize organic matter; this includes photosynthesis by plants and algae and bacterial nitrification of ammonium. Heterotrophic organisms consume organic matter generated by autotrophs and include a wide variety of organisms from bacteria to large invertebrates. This review of literature focuses on major processes that influence nutrient supply and demand in Humboldt Bay. This provides the basis for estimation of the annual and seasonal nutrient mass contribution of each. Previous works conducted in Humboldt are reviewed where available; where no information in Humboldt

Bay is available, literature for nearby estuaries and bays are reviewed.

Figure 11 - Major nutrient sources, types of biological uptake, and sinks for Humboldt Bay.

Nutrient Cycling

At a typical seawater pH of approximately 8, base elemental nutrients carbon, nitrogen, phosphorus, and silicon are present in the water column as various dissolved

2- - inorganic compounds including carbonate (CO3 ), bicarbonate (HCO3 ), ammonium

+ - - (NH4 ), nitrate (NO3 ), nitrite (NO2 ), orthophosphate species including dihydrogen

- 2- phosphate (H2PO4 ) and hydrogen phosphate (HPO4 ), and silicic acid (H4SiO4), as well as numerous dissolved and particulate organic compounds (Millero, 2013). Species of orthophosphate with hereafter be referred to as phosphate and silicic acid will be referred to as silicate. Dissolved inorganic and organic nutrients are of particular interest as they

28 form the foundation of ecosystem food webs that can lead to either healthy or eutrophic systems (Testa et al., 2013). Particulate matter transport is a significant mechanism as both source and uptake for nutrients in systems similar to Humboldt Bay through watershed runoff and ocean exchange (Smith et al., 1996). A brief explanation of the major processes in estuarine nutrient cycling involving key constituents is discussed in the following sections.

Nitrogen Cycle

Nitrogen is an essential component of amino acids and proteins, making it an essential nutrient for biological production (Bianchi, 2013). Nitrogen gas (N2) is the most abundant atmospheric gas, although it is not bioavailable to organisms until it is

+ - converted into a form such as ammonium (NH4 ) or nitrate (NO3 ).

Biological fixation of atmospheric nitrogen (Figure 12, i) in marine environments is typically insignificant unless cyanobacteria make up a significant percentage of planktonic biomass (Howarth et al., 1988). Ammonium assimilation (Figure 12, ii) is the process whereby organisms such as plants and phytoplankton uptake inorganic ammonium, incorporating the already reduced form of nitrogen into organic matter

(Bianchi, 2013). Nitrification (Figure 12, iii) is the multistep process of nitrogen oxidation from ammonium to nitrate, requiring the presence of oxygen and carbon.

Nitrification in marine sediments is an important source of nitrate for denitrification

(Seitzinger, 1988). Assimilatory nitrate reduction (Figure 12, iv) may occur when reduced forms of nitrogen such as ammonium are low and oxygen levels are high. As

29 autotrophic plants and algae preferentially uptake ammonium first, producing oxygen in the process, nitrate may then become an important fraction of bio-available nitrogen

(Bianchi, 2013). Ammonification, or mineralization (Figure 12, v), is the process of organic decomposition by heterotrophic bacteria converting organic nitrogen to ammonium. This process plays an important role in the internal nitrogen cycling of productive marine systems as dissolved and particulate organic matter in the water column and sediments is converted back into inorganic ammonium that becomes re- available for autotrophic assimilation. Ammonium oxidation (Figure 12, vi), or anammox, is the direct oxidation of ammonium with nitrate to form nitrogen gas

(Bianchi, 2013). Limited knowledge currently exists of the mechanisms of this process and the significance of flux rates due to anammox, although one study suggests that anammox was insignificant with respect to denitrification in a eutrophic bay (Thamdrup and Dalsgaard, 2002). Dissolved organic nitrogen (DON) assimilation (Figure 12, viii) is an important component of the nitrogen cycle in marine systems as a source of nitrogen for many heterotrophic organisms and often exceeds the concentration dissolved inorganic nitrogen (DIN), including ammonium, nitrate, and nitrite (Berman and Bronk,

2003).

Denitrification (Figure 12, vii) is the multistep enzymatic process of reducing nitrate-nitrogen to form gaseous constituents including nitrous oxide (N2O) and nitrogen gas (N2) (Bianchi, 2013). Denitrification can be a significant pathway for nitrogen removal from marine systems (Seitzinger, 1988). Denitrification of nitrate to nitrogen gas has been attributed to removal of as much as 40-50% of dissolved inorganic nitrogen

30 input from marine systems. Nitrate may be supplied from nitrifying bacteria in oxic surface layers or diffusion from the water column, though studies have shown that nitrification in sediments is the primary source of nitrate for denitrification in marine sediments. Nitrification can increase during daylight from autotrophic organisms producing oxygen in surface sediments. Denitrification rates are typically greater than nitrate fluxes into sediments indicating nitrate produced in surface layers does not have a net flux into the water column. Overall denitrification rates decrease during daylight due to the increased thickness of oxic surface layers resulting from photosynthesis (Risgaard-

Petersen et al., 1994).

Phosphorus Cycle

The marine phosphorus cycle includes dissolved inorganic phosphorus, organic phosphorus, phosphorus adsorbed to particles, and phosphorus-metal oxide complexes

- (Bianchi, 2013). Dissolved inorganic phosphorus in the form of orthophosphate (H2PO4

2- or HPO4 ) has a higher turnover rate compared to dissolved organic phosphorus, increasing its potential availability as a nutrient source in coastal waters (Benitez-Nelson and Buesseler, 1999). Organic phosphorus can be particulate or dissolved and includes

DNA, cellular membranes, and ATP used by organisms for energy transfer (Bianchi,

2013). Phosphorus-metal oxide complexes, the most common of which is ferric oxyhydroxide, can also be a significant source or uptake for phosphorus dependent upon salinity, temperature, and oxidation-reduction conditions; reducing conditions as a result of anoxia in sediments, can increase phosphorus release (Conley et al., 1995).

Phosphorus concentrations can increase or decrease with suspension of particles as phosphorus adsorbs to, or desorbs from, particle surfaces distributed throughout the water column.

Silicon Cycle

The marine silicon cycle is primarily a function of dissolved silicic acid (H4SiO4) utilized by marine diatoms to synthesize biomass (Paerl and Justic, 2013). Diatoms produce at a very high rate (up to two doublings per day or more) and assimilate silicon in a 1:1 ratio with nitrogen, increasing the importance of this organism in the nitrogen cycle (Brzezinski, 1985). Silicon can come from upwelled ocean waters as well as watershed runoff from weathered geological formations, and the major form of storage is through sedimentation (Bianchi, 2013).

Nutrient Sources and Uptake

Humboldt Bay is a highly productive system in the summer that can become limited by nitrogen and experiences low productivity in the winter due to reduced ocean upwelling, decreased sunlight, and lower temperatures (Pequegnat and Butler, 1981).

Upwelled ocean waters rich in nutrients promote phytoplankton production in nearshore waters during the spring and summer that enter the Bay through tidal interaction.

Phytoplankton from nearshore waters, subtidal eelgrass beds, algae growing on intertidal mud flats, and salt marsh grasses are all primary producers that utilize nutrients and solar energy during the productive upwelling season. Tidal flushing transports nutrients and phytoplankton from nearshore waters into the Bay during the upwelling season, whereas eelgrass, mudflat algae, and salt marsh grasses are all endogenous nutrient consumers originating and growing only inside the Bay (Schlosser and Eicher, 2012).

Nutrient sources to Humboldt Bay may include oceanic exchange, watershed runoff, wastewater inflow, decomposition of organic matter in sediments, and atmospheric fixation. Nutrient uptake and sinks may include oceanic exchange, primary productivity, oyster and fish harvesting, denitrification, and volatilization of gases.

Humboldt Bay is an important habitat for seasonally migrating birds and fish (Barnhart et al., 1992) that may be a significant source of nutrient import or form of uptake and export; however, estimation of the complex migration patterns and behaviors of the numerous species with respect to nutrient cycling is beyond the scope of this project.

Atmospheric Fixation

Carbon and nitrogen are fixed from the atmosphere as carbon dioxide and nitrogen gas, respectively, although nitrogen fixation is likely a minor contributor to overall loadings in nitrogen-limited estuaries (Howarth et al., 1988). Atmospheric nitrogen gas (N2) is fixed by some species of bacteria and algae, although no information is available on the presence or distribution of these species in Humboldt Bay. Fixation rates in oceans and estuaries vary from 0.002-1.8 g N/m2/yr, with estuarine fixation rates typically being higher than those in oceans (Howarth et al., 1988). Carbon dioxide from the atmosphere diffuses into the water column and is consumed by autotrophic organisms during photosynthesis, producing organic carbon. This process is likely the main source of carbon to a highly productive estuarine system such as Humboldt Bay (Bianchi, 2013).

Phytoplankton Production

Phytoplankton production may account for more than half of the total ecosystem primary productivity in coastal systems (Paerl and Justic, 2013), and can be determined by measuring chlorophyll-a concentrations and light penetration into the water column

(Ryther and Yentsch, 1957). High rates of phytoplankton production, determined as chlorophyll-a concentrations, and excessive nutrient availability in estuaries is an indicator of eutrophication (Bricker et al., 2003). Estimates for phytoplankton nutrient assimilation rates vary widely because they have been found to be dependent primarily on nutrient availability and secondarily on light availability (Ryther and Yentsch, 1957;

Curl and Small, 1965). An accurate model for estimating dynamic assimilation rates in

Humboldt Bay has not been established, however, Harding (1973) collected samples at

18 locations throughout the Humboldt Bay system measuring chlorophyll-a and light penetration, and estimated primary production rates for phytoplankton using the methods of Ryther and Yentsch (1957). Primary productivity for phytoplankton was estimated by correlating carbon uptake with chlorophyll-a concentrations, resulting in a mean assimilation ratio of 10.9 g C/hr/g Chl-a, with a range of 1.3-46.8 g C/hr/g Chl-a. Ryther and Yentsch (1957) measured an average phytoplankton uptake rate of 1.7 g C/hr/g Chl-a in the Puget Sound of Washington state, with a range of 0.3 - 5.1 g C/hr/g Chl-a.

Studying waters off the coast of Newport Oregon, Curl and Small (1965) measured assimilation ratios between 6 - 21 g C/hr/g Chl-a, with a mean of 8.1 g C/hr/g Chl-a.

Significant differences in uptake rates are associated with variations in water column nutrient concentrations; values of 0-3 g C/hr/g Chl-a indicate nutrient depletion, 3-5 g

C/hr/g Chl-a indicate borderline nutrient deficiency, and 5-10 g C/hr/g Chl-a indicate nutrient rich waters (Curl and Small, 1965).

Using the widely accepted Redfield ratio of carbon, nitrogen, and phosphorus contained in planktonic biomass of 106:16:1 (C:N:P; Fleming 1940), nitrogen and phosphorus assimilation ratios can also be estimated from chlorophyll-a concentrations

(Table 11). Diatoms are some of the most abundant and fast growing phytoplankton utilizing silicon at a stoichiometric ratio of 1:1 with nitrogen (Brzezinski, 1985). There are no data available on the relative abundance of diatoms and other species of phytoplankton in Humboldt Bay; to account for the likelihood that diatom blooms do occur, silicon uptake is included in phytoplankton assimilation ratios.

Source Location Carbon Silicon Nitrogen Phosphorus Ryther and Puget Sound, 1.7 0.6 0.3 0.04 Yentsch (1957) WA Curl and Small Newport, 8.1 2.9 1.4 0.2 (1965) OR Harding Humboldt Bay, 10.9 3.8 1.9 0.3 (1973) CA

Eelgrass Production

Pequegnat and Butler (1982) estimated that eelgrass production could make up approximately 18% of the total plant production in Humboldt Bay, and eelgrass beds may cover approximately 32% of the surface area of the Bay (Schlosser and Eicher, 2012).

Harding (1973) measured eelgrass biomass in South and North Humboldt Bay between

April and August 1973 estimating a total net production for Humboldt Bay of nearly 22 million kg. The area covered by eelgrass in the Bay at that time was approximately 12.2

Mm2, indicating an annual areal production rate of approximately 565 g/m2/yr. A more recent study conducted found that the eelgrass distribution in the Bay was approximately

22.8 Mm2 (Schlosser and Eicher, 2012), indicating that the eelgrass beds have expanded and a greater amount of eelgrass productivity may be expected.

Macroalgae Production

Pequegnat and Butler (1982) estimated that microalgae and macroalgae growing on the subtidal and intertidal mudflats may account for approximately 37% of the total

36 plant production in Humboldt Bay (8,200 Mg/yr). Schlosser and Eicher (2012) estimated that in late summer and fall of 2007 and 2008, macroalgae covered approximately 12% of the total surface area of Humboldt Bay (8.7 Mm2), or approximately 23% of the intertidal mud flats. The most abundant species were filamentous forms including Chaetomorpha aerea, tubular forms including Ulva intestinalis, and sheet forms including Ulva spp.

Pregnall and Rudy (1985) estimated the production rate of the macroalgal species

Enteromorpha spp. in the Coos Bay estuary in Oregon State of approximately 1,100 g

C/m2/yr. Coos Bay is approximately 150 miles north of Humboldt Bay and likely experiences similar growing seasons. Pregnall and Rudy (1985) observed initial algal growth beginning in April, peaking in August, and ceasing in November; a similar pattern of macroalgal growth has been observed in the Entrance Bay of Humboldt Bay

(Schlosser and Eicher, 2012). Significant inter-annual variability in temporal and spatial distribution of macroalgal mats may occur in Humboldt Bay; though very little information exists on this topic. Schlosser and Eicher (2012) noted a general trend of macroalgal mats persisting for longer periods of time at one site in Humboldt Bay between 2002 and 2008, and noted observations that mats were increasingly noticeable on the intertidal mud flats of Arcata Bay.

Salt Marsh Production

Pequegnat and Butler (1982) estimated that the salt marshes around Humboldt

Bay may contribute 22% of the total plant production and Schlosser and Eicher (2012) estimated that salt marshes make up 5% of the surface area of the Bay (1.41 mi2). Salt

37 marshes lie in the upper intertidal boundaries of the Bay and likely only receive periodic interaction with tidal Bay waters during higher high tides, although rainfall and surface water flow may increase the effects of nutrient export by salt marshes. Salt marshes may provide seasonal storage for dissolved nutrients as plant uptake removes nutrients from tidal and surface waters (Valiela et al., 1978). Marshes can also act as storage for particulate matter when flows are low, and a source for particulate matter when flows are higher, during precipitation and runoff events or high tides. Marshes may import nutrients and particulate matter during the summer growing season when flows are generally lower, and export nutrients during the fall and winter when plants senesce and flows increase.

Mariculture

There are currently approximately 10.42 metric tons (dry weight) of shellfish stock being cultured in Arcata Bay, half of which are harvested each year (H.T. Harvey &

Associates, 2015). This represents a potentially significant sink for nutrients as the oysters filter phytoplankton from the water converting it to biomass that is harvested and exported from the system. Jansen et al. (2012) measured annual nutrient accumulation rates in blue mussels of 560 mg C/g tissue/yr, 168 mg N/g tissue/yr, and 12 mg P/g tissue/yr (a stoichiometric ratio of 47:14:1). If one-half of the oysters are harvested each year (Wagschal, 2015), this would result in a net annual export of 2.918 Mg C/yr, 0.875

Mg N/yr, and 0.063 Mg P/yr.

There are currently two major proposals to expand oyster farming in Arcata Bay by up to six times its current level of production, significantly increasing the amount of nutrients exported from the system through this pathway. Oysters filter particles from the water column to feed. Applying the filtration rate used by H.T. Harvey & Associates

(2015) of 2.54 L/g/hr (Cranford et al., 2011), the current standing stock of oysters in

Arcata Bay (10.42 x 106 g) may be capable of filtering 6.35 x 105 m3 of water each day, or approximately 1% of the MHW volume of Arcata Bay.

Sediment Flux

Sediments can act as source and storage for nutrients with significant seasonal and diurnal variation due to changes in wind patterns, sediment loads, production rates, vegetative cover, temperature, sunlight, oxygen availability, pH, tidal immersion and emersion, and microorganisms living in the sediments (Thompson, 1971; Mackin and

Aller, 1984; Smith et al., 1985; Smith et al., 1996; Sin et al., 2007). Nutrients in suspended sediment loads from creeks and ocean tides can settle over parts of the mud flats in Humboldt Bay with significant seasonal variation due to wind patterns

(Thompson, 1971). Erosion of the mud flats of northern Arcata Bay was witnessed by

Thompson (1971) between November and April due to southerly winds that increase wave erosion across the long fetch of the Bay. Between spring and fall, Thompson

(1971) observed winds prevailing from the north that resulted in less wave erosion in northern Arcata Bay and increased accretion. This behavior was also observed at other locations in the Bay indicating that erosion will occur on the side of the Bay where the

39 prevailing wind direction is over the longest open water fetch, and accretion will occur in locations more shielded from the prevailing wind fetch. These patterns may have significant effects on particulate and dissolved nutrients in the water column as well as sediment nutrient fluxes.

Marine sediments may act as a storage for organic matter as algae and other organisms die and settle out of the water column, while the sediments may act as a source for dissolved inorganic and organic nitrogen as this material is re-mineralized through heterotrophic decomposition. Denitrification in anoxic sediments may be a sink for dissolved inorganic nitrogen, although Sin et al. (2007) indicate that algae covered sediments reduce the sediment-water interface by assimilating nitrate and ammonium from the water column and reducing the ability for these nutrients to reach sediments.

The mud flats of Humboldt Bay experience significant seasonal coverage by macroalgal mats (Schlosser and Eicher, 2012). Areas without macroalgae may be influenced by benthic microalgae (Sin et al., 2007).

North and South Humboldt Bay contain extensive intertidal mud flats that may provide a significant medium for potential nutrient cycling via particle settling and burial, remineralization of nutrients via heterotrophic bacteria, pore water exchange of dissolved nutrients, microalgal photosynthesis at the surface, and microfauna that both consume organic material and burrow through sediments increasing the pore water exchange rates

(Sin et al., 2007). There are no data available on the spatial or temporal distribution of any of these processes in Humboldt Bay, and the wide seasonal distribution of eelgrass and macroalgae over the intertidal mudflats of the Bay further complicate any estimation

40 of sediment nutrient flux due to photosynthetic uptake of sediment nutrient sources

(Larned, 2003). Additional complicating factors include intertidal variation due to immersion and emersion resulting in varying amounts of exposure to sunlight and atmospheric oxygen, diel variation due to sunlight that drives photosynthesis and oxygen production at the sediment-water interface, diel and seasonal gradients in water temperature and salinity due to runoff, upwelling, and evaporation, and nutrient gradients between the sediment and water column due to all of the aforementioned processes

(Garber et al., 1992).

Sin et al. (2007) documented nitrate, ammonium, phosphate, and silicate flux rates in microalgal covered intertidal silt and clay sediments in Yaquina Bay, Oregon, approximately 220 miles to the north of Humboldt Bay (Table 12). Sediment type likely influences sediment nutrient flux as well as vegetative cover such as microalgae, macroalgae, eelgrass, and marsh grasses (Sin et al., 2007). Thompson (1971) described the sediment material of Humboldt Bay's intertidal mud flats as clayey silt with no specification as to organic content, whereas the sediments examined by Sin et al. (2007) were predominantly sand (approximately 70-80%) with 10-20% silt, 7-9% clay, and 0.6-

0.9% total organic carbon content (another site was also included in this study that is omitted from this review because it contained more sand than the other two sites which is less comparable to sediments of the Humboldt Bay mud flats).

Sin et al. (2007) estimated that net nitrate fluxes were always into the sediments from the water column regardless of light exposure (Table 12). During light exposure, algae may uptake nitrate for production, while during dark periods, coupled nitrification-

41 denitrification may be responsible for nitrate removal. Nitrate production via nitrification of ammonium was estimated to be less than the demand for nitrate due to uptake and denitrification resulting in a net negative flux rate during all periods. Sediment ammonium fluxes indicated sediments were a source of ammonium during both light and dark periods, though dark flux rates were generally higher due to reduced algal uptake during photosynthesis. Ammonium efflux from sediments was possibly the result of re- mineralization of ammonium from decomposing organic matter (Kemp et al., 1990).

Phosphate fluxes into sediments were measured during light periods, possibly due to photosynthetic uptake and/or chemical adsorption to oxidized iron (II) present in oxic sediments (Bray et al., 1973). Phosphate fluxes out of sediments were measured during dark periods, possibly due to anoxia resulting from cessation of photosynthesis by overlying algae and plants (Taft and Taylor, 1976). Silicate fluxes varied with light and dark phases, being uptaken by sediments during light phases and released to the water column during dark phases. Silicate uptake was attributed to algal production and release may be attributed to biogenic recycling (Barelson et al., 1987).

Table 12 - Nutrient flux rates for microalgae-covered intertidal sediments in Yaquina Bay, Oregon (mg/m2/hr); negative values denote sediment uptake.

Photoperiod Nitrate-N1 Ammonium-N1 Phosphate-P1 Silicate-Si1 -1.40 to -0.15 -0.73 to 0.60 -0.23 to 0.03 -2.61 to 0.00 light (-0.39) (-0.06) (-0.08) (-1.29) -1.71 to -0.13 -0.05 to 1.41 -0.06 to 0.37 -0.81 to 7.95 dark (-0.45) (0.43) (0.11) (2.39) 1Sin et al. (2007)

Denitrification

In a survey of six estuaries, Seitzinger (1988) estimated that denitrification may be responsible for 20-50% removal of all nitrogen inputs. Few studies have directly measured denitrification rates in estuaries of the eastern Pacific coast; although many different analytical techniques have been developed to measure denitrification with varying accuracy. Denitrification rates between 0.70-3.50 mg N/m2/hr have been measured in other estuaries and bays around the world (Seitzinger, 1988), although most of these systems are on the Atlantic Ocean and may have limited applicability to systems on the northeastern Pacific coast. The highest rates of denitrification occur in eutrophic waters with high nutrient loads and low oxygen. Of the systems presented by Seitzinger,

Oremland et al. (1984) measured denitrification rates in intertidal sediments of San

Francisco Bay between 0.02-0.05 mg N/m2/hr in San Francisco Bay following the acetylene inhibition methodology described below.

Denitrification in intertidal sediments covered by marine vegetation such as eelgrass and algae is complicated by the ammonium uptake and oxygen generation by the plants during photosynthesis (Risgaard-Petersen et al., 1994). During the summer and fall in Humboldt Bay, algae may cover approximately 23% and eelgrass another 59% of the mud flats (Schlosser and Eicher, 2012); this does not include the rest of the mud flats that may be covered in microalgae including benthic diatoms. Oxygen generation by macroalgae during photosynthesis has been found to reduce denitrification of nitrate from the water column by approximately 60% (Risgaard-Petersen et al., 1994); however,

43 during both light and dark periods, nitrate from the water column made up 73% and 92% of nitrate used for denitrification, respectively.

Multiple methods have been used to determine denitrification rates in marine systems including a system-wide mass balance approach, inference from nitrate removal in overlying waters, laboratory measurements of gas production, and inference from stoichiometric nitrogen-phosphorus ratios in sediment pore water (Seitzinger, 1988). The mass balance approach infers the amount of nitrogen lost due to denitrification from a mass balance of inputs and outputs; any nitrogen that is not accounted for in the mass balance is attributed to denitrification. This method may only be as accurate as the estimates for other sources and sinks in the mass balance and does not account for spatial variability or identify specific processes involved in denitrification (Seitzinger, 1988).

Denitrification rates are also inferred from decreases in nitrate or nitrite concentrations in the overlying water column assuming nitrate loss is due to denitrification. This method may overestimate denitrification rates because it does not account for other processes that are involved in nitrate production and removal such as nitrate reduction to ammonium, or plant uptake, and nitrification in oxic layers of sediments respectively (Seitzinger, 1988).

Analytical laboratory techniques have also been developed to directly measure the products of denitrification including nitrous oxide and nitrogen gas. One method measures nitrous oxide production as an indicator of denitrification (the precursor to nitrogen gas in the denitrification process) by inhibiting the final stage of nitrogen gas production using acetylene (Balderston et al., 1976; Yoshinari and Knowles, 1976). This

44 method has been found to be problematic as acetylene incompletely inhibits reduction of nitrous oxide under certain conditions and also inhibits nitrification (Hynes and Knowles,

1978). Denitrification in sediments can be directly linked to nitrification in which case this method would underestimate denitrification (Seitzinger, 1988). Direct measurement of nitrogen gas produced from sediments is complicated by the fact that nitrogen is the most abundant gas in our atmosphere, creating the potential for contamination; however,

Seitzinger (1980) has established a method for this technique that eliminates contamination.

Other researchers have estimated denitrification for a whole estuary from nonconservative dissolved inorganic nitrogen fluxes (Smith et al., 1987). A detailed nitrogen budget is constructed where DIN import is compared with storage and export of organic and inorganic nitrogen, and any unaccounted-for DIN is assumed to be lost to denitrification. Using this method Smith et al. (1991) estimated denitrification rates in

Tomales Bay, California (approximately 200 miles south of Humboldt Bay) of 1.81 mg/m2/hr. An accurate nitrogen budget requires a wide variety of data including dissolved and particulate organic nitrogen, dissolved inorganic nitrogen, sediment- nitrogen flux rates, suspended sediment nitrogen content, benthic plant nitrogen content, atmospheric nitrogen fixation, and a water budget including an estimation of tidal flushing.

In a parallel study in Tomales Bay following the work of Smith et al. (1991),

Dollar et al. (1991) directly measured sediment nutrient fluxes. Applying stoichiometric principles of carbon, nitrogen, and phosphorus content of planktonic material (106:16:1,

C:N:P) Dollar et al. determined a sediment denitrification rate of between 0.70-0.76 mg

N/m2/hr.

Humboldt Bay Flushing Times

Various estimates of flushing times in Humboldt Bay between 1 and 30 days have been derived using multiple approaches. Gast and Skeesick (1964) estimated a flushing rate for Humboldt Bay of approximately 8 days ±50% (15 tide cycles, or 0.07 replacement per tide cycle). This approach estimates the freshwater volume in the Bay using the difference between an average salinity and a maximum salinity, and then divides this by the total freshwater inflow during a single tide cycle (Equation 1) to determine how many tide cycles are required for full replacement of the freshwater fraction in the Bay. Gast and Skeesick cite Ayers (1956) as their source for this approach although Ayers cites the work of Ketchum (1951) as the originator of this approach. This approach may be more applicable for estuaries where high rates of freshwater inflow are the dominant source of water, whereas in Humboldt Bay this is not the case.

Gast and Skeesick (1964) noted that higher salinity occurred inside Arcata Bay during the summer and fall due to evaporation, and lower salinities occurred inside

Arcata and South Bays during the winter and spring due to precipitation and runoff.

After significant dilution during the wet season in Arcata and South Bays, salinities returned to values measured at the Bay entrance approximately four months and two months later, respectively indicating that Arcata Bay has a much lower flushing rate than

South Bay, though the flushing rates of both bays are quite low.

푆 − 푆 ( 푚푎푥 푎푣) ∗ 푉 푆 ℎ𝑖𝑔ℎ (1) 푡 = 푚푎푥 푄𝑖푛

Where, t = tidal flushing time (number of tide cycles)

Smax = maximum salinity (ppt)

Sav = average salinity (ppt) 6 3 Vhigh = high tide volume (10 ft ) 6 3 Qin = total freshwater inflow per tide cycle (10 ft /cycle)

Casebier and Toimil (1973) estimated flushing times for Arcata Bay using three different methods. During the low flow summer season, a flushing time of approximately one day (2.1 tide cycles, or 0.48 replacement per tide cycle) was calculated (Equation 2).

This approach assumes complete mixing of the tidal prism, likely resulting in a very low estimate of the exchange rate. It is unclear what volumes were used for the Bay and tidal prism in their calculations; the volume used (V) should have been the high tide volume and not the low tide volume (Ketchum, 1951); this would result in a significant underestimate of the flushing time. During the winter runoff season, a flushing time of approximately 0.4 days (0.8 tide cycles, or 1.25 replacement per tide cycle) was calculated using the same approach applied by Gast and Skeesick (1964) above in

Equation 1 from Ketchum (1951). A third approach was applied that models salinity gradients along a longitudinal pathway incorporating a dispersion term that may increase the flushing time depending upon the value used (which was not specified). Model results with F=0.08 (0.08 replacement per tide cycle, 12.5 tide cycles, or approximately 6

47 days) indicated the best fit to observed measurements. Their calculations are reportedly within an order of magnitude meaning their estimates for exchange rates range from 2.4 hours to 10 days during the summer and from one hour to 60 days during the winter.

푉 − 푃 푡 = (2) 푃

Where, t = tidal flushing time (number of tide cycles) V = high tide volume (103ac ∙ ft) P = tidal prism (103ac ∙ ft)

Costa (1982) estimated a flushing time for Mad River Slough of approximately 43 days (85 tidal cycles, or 0.01 replacement per tide cycle), and indicated that Arcata Bay would likely have a flushing time much less. No details were provided for the method employed to calculate the Mad River Slough flushing time.

ANATEC Laboratories (1982) conducted a tracer dye study in Arcata Bay estimating 99% replacement in 16.4 days (approximately 33 tide cycles, or 0.03 replacement per tide cycle). During this study, wind and rain from a February storm may have interrupted the normal flow patterns in the Bay as well as causing vertical stratification due to salinity differences between increased freshwater runoff and the Bay water. The results were not used in any type of advanced mathematical or computational model due to budget and time restrictions, although the longer replacement times found

48 during a winter storm indicate previous estimates of flushing times are likely significantly low.

Using a three-dimensional hydrodynamic model, Anderson (2010) estimates 90% flushing times for Arcata Bay to be over 30 days (0.02 per tide cycle), for Entrance Bay to be 1.6 days (0.31 per tide cycle), and South Bay to be 14 days (0.04 per tide cycle).

The simulation runs that resulted in these estimates ran for one month from June to July

2009, and may represent a lower estimate due to low streamflow to the Bay during this summer period. The model package consists of an open source numerical model called

Environmental Fluid Dynamics Code (EFDC) built for the US EPA and run by a proprietary interface program called EFDC Explorer by Dynamic Solutions International that allows advanced input and output processing (Craig, 2013). The three-dimensional finite difference hydrodynamic model is a formulation of the three-dimensional navier- stokes equations of fluid motion and incorporates many fluid properties including temperature, salinity, viscosity, eddy diffusivity, and bottom roughness to increase the accuracy of simulated fluid motion (Hamrick, 1992). The hydrodynamic model contains

1,475 horizontal segments with an average size of 210 m by 230 m, and each cell is divided into three vertical layers. The relatively small resolution of the spatial cells

(previous approaches treat the entire Bay as one cell), addition of realistic physical properties of fluid motion, and use of a dynamic finite difference numerical solution approach makes estimates from this model much more robust than previous approaches to estimating flushing times. The model has been calibrated using continuously monitored data from the NOAA North Spit station, South Bay, and Mad River Slough

(Anderson, 2010). The model also incorporates forcing functions including tidal elevation and temperature at the Bay entrance, tributary streamflow from creeks emptying into Humboldt Bay, and atmospheric data including air temperature, relative humidity, wind speed and direction, atmospheric pressure, solar radiation, and cloud coverage. It should be noted that the model has only been roughly calibrated at a few locations in the Bay and may undergo further calibration and verification.

Humboldt Bay Circulation Studies

Horizontal and vertical circulation patterns in Humboldt Bay have been documented using naturally occurring water quality parameters such as salinity, temperature, dissolved oxygen, and dissolved nutrients. Additional horizontal circulation patterns have been documented using tracer dyes and drift poles that provide information about velocity and distribution of water currents that are more difficult to determine using constituents that exist everywhere naturally such as salinity. Gast and Skeesick (1964) documented the seasonal patterns of horizontal and vertical stratification that occur with respect to salinity due to increased freshwater inflow during the winter runoff season and with respect to temperature in the summer due to sunlight heating water over the shallow mud flats and reduced runoff. Vertical stratification tends to be very weak in Humboldt

Bay during the winter due to the shallow inner bays and high rate of mixing that occurs in the channels due to the large tidal prisms and wind driven mixing. Due to the weak stratification of the Bay during storms and the vertical homogeneity that exists during the rest of the year, the Bay is assumed to be vertically homogeneous for the purposes of this

50 project. Gast and Skeesick (1964) also conducted a tracer study sometime between 1961 and 1964, documenting bulk circulation patterns using drift poles and tracer dye. Drift poles were tracked from the shore and used to indicate flow direction while the tracer dye was used to document bulk circulation patterns and current velocity. Results of these studies were not presented with any advanced numerical analysis with respect to flushing times or mixing rates.

Klamt (1979) documented the potential for wastewater discharged from Arcata and Eureka to reach oyster beds in Arcata Bay within a single tide cycle using a fluorescent tracer dye during April 1979. While streamflow conditions were not documented, streamflow into the Bay may have been elevated due to the study occurring during the spring after winter rainfall in the watershed increases stream flows. No appreciable rainfall occurred during the study indicating there may have also been an absence of wind-driven mixing from storm conditions. One study injected dye at the decommissioned Hill Street wastewater treatment facility (WWTF) at high tide and measureable amounts of dye were detected near the Murray Street WWTF (also decommissioned) at the slack tide (Figure 13). This dye study documented the relative isolation of Freshwater Creek/Slough effluent from Arcata Bay. A second dye study injected dye into the old AWTF effluent near high tide (near the south end of what is now

Oxidation Pond 1) and measureable amounts were detected approximately 2.5 miles downstream near the center of Arcata Bay at slack tide (Figure 13). This study illustrates the relative isolation of Arcata Bay such that discharge from the AWTF will not exit

Arcata Bay on a single tide cycle. A third dye study injected dye into the effluent of the

51 decommissioned Murray Street WWTF in Eureka near low tide and measureable amounts were detected far into Arcata Bay in both the Jacoby Creek branch of the Arcata

Channel and the Mad River Slough Channel (Figure 13). This study illustrates the potential for water in the Main Channel to reach far into Arcata Bay on flood tides.

Figure 13 - Three short-term tracer dye studies conducted in Arcata Bay to determine the extent of potential treated wastewater contamination of oyster beds (adapted from Klamt, 1979).

ANATEC Laboratories Inc. et al (1982) conducted a fluorescent tracer dye study in Arcata Bay during February and March of 1982. The dye was injected at the confluence of the Arcata Channel and Jacoby Creek Channel in the northwestern part of

Arcata Bay. Dye was injected continuously for five days attempting to reach a steady state concentration in the Bay after which a die-off could be monitored that would indicate a flushing rate for the Bay. Due to tidal exchange, surface runoff, and subsequent storm events, a steady state dye concentration was not reached and the team resigned to monitoring the die-off of the dye that had been injected in the first five days of the study. Samples were collected from the surface and at 3 m depth from 50 locations at high and low tides during daylight hours. During this period multiple storm events occurred, introducing moderate winds and heavy rainfall, complicating sampling, diluting

Bay waters, increasing runoff, and altering mixing patterns due to wind-driven mixing.

Findings of the ANATEC Laboratories et al. (1982) tracer study indicate that rainfall and increased runoff during the storm events were sufficient enough to dilute the salinity in Arcata Bay to approximately 25 ppt, although vertical stratification was also observed, whereby bottom salinities were closer to 29 ppt. This vertical stratification marked a difference between landward freshwater inputs and seaward saltwater flows that were tracked as the saltwater front moved into Mad River Slough Channel and

Arcata Channel over the following three days. This finding is significant with respect to tidal flushing as increased streamflow and rainfall might theoretically decrease the residence time in Arcata Bay, when in reality the difference in water density caused by rainfall might actually act to further isolate waters within the Bay. However, wind events

53 blowing from the east resulted in transport of dye from its origins in the east side of

Arcata Bay to the western side faster than expected. Dye concentrations in the Arcata

Channel and Mad River Slough Channel were very similar likely due to the confluence of these two channels in the Samoa Channel during each ebb tide cycle which results in near complete mixing. Waters in the southeastern portion of the Bay including

Indian/Woodley Island Channel and Eureka Channel were isolated from dyes in the rest of the Bay, showing up one and two days after the other two, respectively, indicating that these channels are relatively isolated from the main channels of the western portion of the

Bay that converge into the Samoa Channel.

In March 2004 the California Department of Health Services conducted a fluorescent tracer dye study in Arcata Bay during low streamflow conditions at Gannon

Slough, Eureka Slough, and Butcher's Slough (CDHS, 2006). Conditions and results from this study closely follow those of Klamt (1979). Dye injected at Butcher's and

Gannon Sloughs during ebb tides indicate that limited transport occurs across the mud flats separating Arcata Channel and Mad River Slough Channel, and that dye was not transported far enough out of the Bay to reach the confluence of the two channels where direct mixing could occur. Dye was injected at the railroad bridge in Eureka Slough on an ebb tide and reached the mouth of the Bay during a single ebb tide cycle. This is a much greater distance than observed by Klamt (1979) during the dye study conducted from the former Hill Street WWTF located near the railroad bridge in Eureka Slough.

While it is not clear what the change in tidal elevation was during March 2004 study, the tidal range during the April 1979 study was only 2.8 feet following the lower high tide.

This may indicate that during a larger tidal ebb, water may flow from Eureka Slough all the way to the mouth of the Bay, whereas during a minor tidal ebb, water may not reach much past the confluence of the Samoa Channel and Eureka Channel (Figure 13). This finding is significant with respect to the degree to which water from Freshwater Slough interacts with the rest of Arcata Bay. CDHS (2006) measured the dye plume from the

Eureka Slough injection in the Mad River Slough Channel and Arcata Channel during the subsequent flood tide indicating that during larger tidal cycles constituents from different reaches of the Bay may be interacting. The tidal characteristics of Humboldt Bay are characterized by semidiurnal inequality (Barnhart et al., 1992); generally containing a higher high, higher low, lower high, and lower low tide each day. This results in one tidal elevation change being greater or less than the following one. This characteristic significantly complicates mixing and tidal flushing characteristics of the Bay.

Humboldt Bay Nutrient Studies

Gast (1962) collected an extensive set of nutrient data for Humboldt Bay including depth, temperature, chlorinity, salinity, density, dissolved oxygen, phosphate-P, and silicate-Si. Monthly samples were collected at 12 sites throughout the Humboldt Bay system and one site outside the mouth of the Bay from September, 1961 to September,

1962 (n = 503). This study did not measure nitrogenous constituents (ammonium, nitrate, and nitrite) which have subsequently been determined to be the primary limiting nutrient in Humboldt Bay (Pequegnat and Butler, 1981). Samples were also collected at multiple depths supporting the conclusion that vertical homogeneity exists throughout the

Bay due to the large tidal prism and strong mixing on flood and ebb tides (Gast and

Skeesick, 1964). The ranges of silicate and phosphate measured by Gast (1962) are listed in (Table 13). Concentrations of silicate and phosphate near the Bay entrance were higher than those inside the Bay during September and October of 1961 and again between March and May of 1962 which were attributed to ocean upwelling events.

Table 13 - Phosphate and silicate concentration ranges measured near the Bay entrance, in Arcata Bay, and in South Bay.

Location Units Phosphate-P1 Silicate-Si1 µM 1.1 - 3.0 8.6 - 40.2 Bay Entrance (µg/L) (35.3 - 93.9) (242 - 1,129) µM 1.4 - 2.8 13.9 - 40.1 Arcata Bay (µg/L) (44.6 - 87.7) (390 - 1,126) µM 1.3 - 3.2 15.5 - 39.6 South Bay (µg/L) (41.2 - 98.2) (435 - 1,112) 1Gast (1962)

Janeway (1981) sampled seven locations around the perimeter of Arcata Bay, one location along the Main Channel, and near the Entrance Bay, and two locations along the shore of the Samoa Peninsula 17 times between July 1979 and March 1980 (n = 187).

Samples were collected at the lowest tides twice per month to measure water flowing into the Bay from tributaries and the AWTF as well as measuring water leaving the Bay, and flowing into the ocean. Samples were analyzed for ammonium-N, nitrate-N, phosphate-

P, dissolved oxygen, water temperature, conductivity, and pH. This study was conducted to help the City of Arcata establish its natural wastewater treatment system rationale for

56 discharging into Arcata Bay. The ranges of nutrients measured in the Bay by Janeway

(1981) are listed in Table 14.

Data collected by Janeway (1981) indicate that no upwelling conditions were experienced during the study; there were no decreases in water temperature and corresponding increases in salinity and nutrients near the Bay entrance. The typical upwelling season is March or April through September, with maximum upwelling typically occurring in June or July according to average monthly upwelling indices

(PFEL, 2015); this may indicate that upwelling occurred prior to July 1979 or after

March 1980. Because of this, nutrient concentrations were consistently higher near the sloughs of the Bay than inside the Bay or near the Bay entrance. Data collected at six locations near the sloughs surrounding Arcata Bay are in good agreement indicating nitrate concentrations were higher during the fall and winter runoff season; approximately 0.5 mg/L as N (36 µM) compared to approximately 0.1 mg/L as N (7 µM) during the rest of the study period. Janeway attributed the higher levels of nitrate during the runoff season to oxidation of fecal material from pasturelands and septic systems as well as urban runoff. Phosphate concentration data from the six slough stations around

Arcata Bay were in generally good agreement with the exception of data from Gannon

Slough that were significantly higher than all other stations during three sample periods in August, September, and October 1979. Omitting that exception, phosphate concentrations were higher during July and August only; approximately 0.25 mg/L as P

(8 µM) compared to approximately 0.1 mg/L as P (3 µM) during the rest of the study period. High values measured near Gannon Slough were closer to 0.7 mg/L as P (23

µM); the higher values near Gannon Slough may be due to the large size of the Jacoby

Creek watershed. Janeway attributed the depressed concentrations of phosphate during the runoff season to dilution from rainfall. Ammonium concentration data were also in generally good agreement with the exception of Gannon Slough and Freshwater Slough.

Ammonium concentrations at the stations that were in agreement were generally higher during July and August, approximately 0.1 mg/L as N (7 µM), falling to approximately

0.05 mg/L as N (4 µM). Ammonium concentrations near Gannon Slough and Freshwater

Slough were significantly higher than other stations during the late summer and fall; approximately 0.7 mg/L as N (50 µM) and 0.4 mg/L as N (29 µM), respectively.

Janeway attributed the lower levels of ammonium during the winter runoff season to dilution from rainfall.

Janeway (1981) measured three sample locations near the Bay entrance showing relatively good agreement with respect to phosphate and nitrate, although ammonium concentrations show questionable variability and magnitude, being far greater than have been reported by any other source. Phosphate does not show much variation near the Bay entrance remaining approximately 0.07 mg/L as P (2 µM) throughout the study period.

Nitrate rose from approximately 0.04 mg/L as N (3 µM) to approximately 0.08 mg/L as

N (6 µM) from October through January. Upwelled nitrate concentrations in nearshore waters of this region of the Pacific Ocean can reach 0.5 mg/L as N (34 µM) indicating these levels are not the result of strong upwelling (Sigleo et al., 2005). Ammonium concentrations near the Bay entrance were higher during August and September reaching

0.3 mg/L as N (24 µM) but remaining much lower during the rest of the study period, less than 0.05 mg/L as N (4 µM).

Table 14 - Phosphate, nitrate, and ammonium concentration ranges (and medians) measured near the Bay entrance and inside Arcata Bay between July 1979 and March 1980.

Location Units Phosphate-P1 Nitrate-N1 Ammonium-N1 1.3 - 4.8 0.7 - 8.6 0.7 - 24.3 Bay Entrance µM (2.3) (3.6) (2.9) 40 - 150 10 - 120 10 - 340 Bay Entrance µg/L (70) (50) (40) 1.3 - 25.2 0.7 - 47.8 0.7 - 85.7 Arcata Bay µM (2.6) (6.4) (3.6) 40 - 780 10 - 670 10 - 1,200 Arcata Bay µg/L (80) (90) (50) 1Janeway (1981)

Pequegnat and Butler (1981) sampled six locations throughout Humboldt Bay twice in 1980 (n = 12); once during an upwelling period, and once during a non- upwelling period. Samples were analyzed for nitrate, nitrite, ammonium, phosphate, and silicate. They determined that nitrogen can become the limiting nutrient during periods of high productivity in Humboldt Bay, indicating that an increase in nitrogen supplied to the system may result in increased biological production. They also estimated that the

AWTF and EWTF were discharging enough nitrogen to Arcata Bay and the Main

Channel to increase the concentration in that part of the system by 0.5 µM (7 µg/L); though there is no indication as to where data came from for this calculation. This implies a wastewater discharge nitrogen load of between 0.336-0.596 Mg N/d, assuming a MLLW volume of 48 Mm3 and a MHW volume of 85.1 Mm3, respectively (Shapiro

59 and Associates, Inc., 1980). Ranges of nutrient concentrations measured by Pequegnat and Butler (1981) are listed in Table 15.

Table 15 - Phosphate, nitrate, ammonium, and silicate concentration ranges (and means) measured near the Bay entrance, in Arcata Bay, and in South Bay.

Location Units Phosphate-P1 Nitrate-N1 Ammonium-N1 Silicate-Si1 1.87 - 2.23 0.5 - 2.6 1.1 - 1.5 22.9 - 26.9 Arcata Bay µM (2.09) (1.4) (1.3) (24.9) 57.92 - 69.07 7.0 - 36.4 15.4 - 21.0 643.2 - 755.5 Arcata Bay µg/L (64.66) (19.6) (17.9) (698.6) 1.27 - 1.90 0.5 - 4.0 0.8 - 2.3 13.5 - 21.9 Main Channel µM (1.59) (2.3) (1.6) (17.7) 39.34 - 58.85 7.0 - 56.0 13.5 - 21.9 379.2 - 615.1 Main Channel µg/L (49.09) (31.5) (17.7) (497.1) 0.03 - 1.44 0.3 - 12.6 0.0 - 1.9 2.1 - 19.2 Bay Entrance µM (0.74) (6.5) (0.95) (10.7) 0.93 - 44.6 4.2 - 176.5 0.0 - 26.6 59.0 - 539.2 Bay Entrance µg/L (22.8) (90.3) (13.3) (299.1) 0.73 - 1.44 0.0 - 2.1 0.2 - 1.5 7.7 - 16.5 South Bay µM (1.08) (1.4) (0.8) (12.0) 22.61 - 44.60 0.0 - 29.4 2.8 - 21.0 216.3 - 463.4 South Bay µg/L (33.45) (19.6) (10.9) (337.0) 1Pequegnat and Butler (1981)

Pequegnat and Butler (1982) estimated plant production in Arcata Bay for a 150 day period between early spring and early fall indicating that 22% (5 million kg), 23%

(5.2 million kg), 18% (4 million kg), and 37% (8.2 million kg) are attributable to salt marsh, phytoplankton, eelgrass, and mudflat algae, respectively; the methods used to determine these values is not indicated. Chlorophyll and nutrient concentrations were greater in nearshore waters during upwelling events indicating this as the source of nutrients and phytoplankton. Compared with values in nearshore waters, chlorophyll

60 concentrations inside the Bay were lower during the spring and summer; this was attributed to nutrient-limitation. During the winter, productivity in and out of the Bay was lower than in the spring and summer upwelling season. However, in the late winter, chlorophyll production inside the Bay began before production outside the Bay; this was attributed to shallow water over the mud flats of the Bay where phytoplankton could be exposed to sunlight whereas in the deeper nearshore waters, phytoplankton may be transported below the photic zone decreasing production.

Henderson (2004) conducted a survey of water quality parameters in the Salmon

Creek watershed of South Humboldt Bay to determine impacts from forestry and dairy activities. Ammonia-nitrogen remained below detection (0.5 mg N/L, 35.7 µM) in all samples from the headwaters to the NWR. Henderson notes that the detection limit of

0.5 mg N/L was too high for this type of study though this indicates ammonia-nitrogen levels were not excessively high in Salmon Creek. Henderson also notes that the dairy operations adjacent to and upstream of sample locations ceased prior to the study such that this study was unable to determine potential water quality impacts from dairy operations. The extent of agricultural impacts to nutrients in creeks around Humboldt

Bay is not well documented.

Tennant (2006) sampled 21 locations around the perimeter of Humboldt Bay and

4 locations outside the Bay on the shorelines north and south of the Bay entrance.

Measurements of ammonium, nitrate, and phosphate were collected in the water column over a period of one year (n = 300) and the data were segregated into a wet season

(November through May) and a dry season (June through October). An unknown

61 number of sediment pore samples were also collected from various sites throughout the

Bay during this study and analyzed for nitrogen and phosphorus content. This work addressed how ammonium, nitrate, and phosphate levels in the water and sediment affect eel grass density in Humboldt Bay. Tennant concluded that nitrogen and phosphorus supplied to eelgrass through the sediments were sufficient to meet saturation levels for eelgrass growth and that concentrations in the water column were not likely the direct cause of eelgrass density variation. The greatest concentrations of nitrate were observed near the Bay entrance during the dry season which may indicate upwelling was a dominant source of nitrate to the Bay during this study (Table 16 and Table 17). Nitrate concentrations inside the Bay were higher during the runoff season than during the dry season possibly due to low productivity. Phosphate concentrations remained relatively low and steady throughout the Bay and during each season. Ammonium concentrations were also relatively low and steady through the Bay for the duration of the study with the exception of March and April when concentrations seemed to increase at some locations in the Bay and not others; the reason for the sporadically high ammonium data is unclear.

Hurst (2009) measured nitrate, nitrite, phosphate, silicate, temperature, salinity, pH, turbidity, and dissolved oxygen at three locations in Humboldt Bay between October

2007 and July 2009. Data collected between October 2007 and October 2008 were published in a poster presentation (Martin and Hurst, 2008) while the rest of the data remain unpublished. Martin and Hurst (2008) measured higher concentrations of nitrate and silicate near Mad River Slough during the runoff season indicating that land-based sources may be significant in Humboldt Bay. These data also support the previous

62 conclusion by Pequegnat and Butler (1981) that nitrate-nitrogen is the limiting nutrient to productivity in Humboldt Bay. Ranges of nutrients measured in Humboldt Bay by Hurst

(2009) are listed in Table 18.

Previous studies in Humboldt Bay have documented seasonal patterns of upwelling and the influences of runoff with respect to nutrients, salinity, and temperature.

However none of these previous studies have included information on wastewater discharges or the flow rates of various sources so that a comparison of relative masses associated with the sources could be evaluated. Many of these studies were conducted over thirty years ago such that any conclusions drawn may not be relevant to present conditions. Previous studies have also failed to quantify in detail, estimations of nutrient uptake to allow a relative comparison to nutrient sources to provide a basis for establishing potential biological and water quality impacts of sources.

This study will combine recent nutrient data from Humboldt Bay and WWTFs with hydrodynamic simulation model flow rates and stream flow estimations to calculate current nutrient loading to Humboldt Bay. This study will also estimate nutrient uptake by major biological processes using recent measurements of chlorophyll-a, eelgrass, and macroalgae distribution in the Bay for comparison to major inputs. Data will be gathered from intertidal samples (adjoining high and low tide samples) collected along a transect between the Bay entrance and Arcata Bay to investigate internal nutrient and phytoplankton dynamics. These samples will provide evidence of internal nutrient dynamics in the Bay to support conclusions about sources and uptake that boundary values collected at one tide stage weeks apart may not suffice to explain.

Location Units Phosphate-P1 Nitrate-N1 Ammonium-N1 0 - 11 0 - 5 0 - 20 Arcata Bay µM (3.8) (1.7) (2.7) 0 - 341 0 - 70 0 - 280 Arcata Bay µg/L (116) (24) (38) 1 - 6 1 - 18 1 - 6 Central Bay µM (3.3) (9.7) (2.4) 31 - 186 14 - 252 14 - 84 Central Bay µg/L (102) (137) (33) 1 - 7 11 - 28 1 - 18 Bay Entrance µM (3.5) (18.0) (3.1) 31 - 217 154 - 392 14 - 252 Bay Entrance µg/L (109) (252) (44) 0 - 25 0 - 13 0 - 13 South Bay µM (3.6) (2.7) (2.0) 0 - 774 0 - 182 0 - 182 South Bay µg/L (113) (38) (28) 1Tennant (2006)

Location Units Phosphate-P1 Nitrate-N1 Ammonium-N1 1 - 10 0 - 25 0 - 33 Arcata Bay µM (3.2) (7.6) (6.5) 31 - 310 0 - 350 0 - 462 Arcata Bay µg/L (99) (107) (91) 1 - 12 0 - 15 0 - 29 Central Bay µM (2.5) (8.9) (5.8) 31 - 372 0 - 210 0 - 406 Central Bay µg/L (78) (125) (82) 1 - 3 3 - 16 0 - 42 Bay Entrance µM (2.0) (8.9) (6.4) 31 - 93 42 - 224 0 - 588 Bay Entrance µg/L (63) (125) (89) 1 - 12 0 - 19 0 - 44 South Bay µM (3.2) (8.0) (8.1) 31 - 372 0 - 266 0 - 616 South Bay µg/L (898) (113) (113) 1Tennant (2006)

Table 18 - Ranges (and medians) of phosphate, nitrate, nitrite, and silicate measured in Humboldt Bay.

Location Units Phosphate-P1 Nitrate-N1 Nitrite-N1 Silicate-Si1 0.4 - 2.1 2.2 - 24.3 0.1 - 0.5 5.4 - 43.4 Bay Entrance µM (1.2) (12.3) (0.3) (16.0) 12.4 - 245 30.8 - 556 1.4 - 7.0 152 - 1,219 Bay Entrance µg/L (37.2) (172) (4.2) (449) 0.5 - 2.6 0.0 - 20.8 0.1 - 0.4 3.8 - 37.1 Indian Island µM (1.3) (6.7) (0.3) (18.1) 15.5 - 80.5 0.0 - 291 1.4 - 5.6 107 - 1,042 Indian Island µg/L (40.3) (93.8) (4.2) (508) 0.8 - 2.9 0.0 - 20.9 0.1 - 0.5 2.8 - 66.3 Mad River Slough µM (1.5) (2.7) (0.2) (16.8) 24.8 - 89.8 0.0 - 293 1.4 - 7.0 79 - 1,862 Mad River Slough µg/L (46.5) (37.8) (2.8) (472) 1Hurst (2009)

METHOD

Sample Collection

Six water quality data sets contributed to this work:

1. Grab samples collected at ten locations inside of Humboldt Bay (Figure 14) by

boat between January 2014 and February 2015. On each sample day, one sample

was collected within one hour of high tide and another sample was collected at the

same location within one hour of low tide for a total of 20 samples on each day

(n=238). Adjacent high and low tides were sampled each day with the exception

of one low tide sample collected on the afternoon of 12/30/2014 and one high tide

sample collected on the morning of 12/31/2014 with one full tide cycle in

between. Temperature, dissolved oxygen (DO), and salinity of these samples

were determined in the field. Determination of pH, total suspended solids (TSS),

turbidity, chlorophyll-a, dissolved organic carbon (DOC), silicate, nitrate, nitrite,

ammonium, and phosphate for the samples was performed in the laboratory.

2. Grab samples collected by Humboldt State University Professor of Chemistry

Matthew Hurst's student research team every two weeks at up to seven freshwater

creek inlets around the perimeter of the Bay (Figure 15) between October 2012

and December 2014 (n=250). Temperature, DO, and salinity of these samples

were determined in the field. Determination of pH, TSS, turbidity, chlorophyll-a,

DOC, silicate, nitrate, nitrite, ammonium, and phosphate for the samples was

performed in the laboratory.

3. Grab samples collected by the Wiyot Tribe's Natural Resources Department every

two weeks at up to five locations in and around Humboldt Bay near high tide

(Figure 16). Three of the locations were collected by boat inside of the Bay (Bay

Entrance, Samoa Channel, and Indian Island), the Mad River Slough sample was

collected from the railroad bridge crossing on Highway 255, and Hookton Slough

was collected at a dock in South Bay the day prior to the other samples, also near

high tide. This dataset includes two separate time periods, October 2007 to July

2009 (three locations inside the Bay, n=138), and October 2012 to February 2015

(five locations, n=285). Temperature, DO, and salinity of these samples were

determined in the field, and determination of pH, silicate, nitrate, and phosphate

was performed in the laboratory. For October 2012 to February 2015,

determination of TSS, turbidity, chlorophyll-a, DOC, nitrite, and ammonium was

performed in the laboratory.

4. In-situ measurements from a multi-instrument data sonde deployed by the Wiyot

Tribe's Natural Resources Department on a fixed pier on the eastern shore of

Indian Island (Figure 14 and Figure 16), taking readings every 15 minutes since

December 2004. Readings include temperature, salinity, DO, pH, turbidity,

depth, and chlorophyll-a. Laboratory determination of chlorophyll-a and field

determination of temperature, salinity, and DO from grab samples in the other

data sets were used to calibrate the data sonde.

5. AWTF effluent (Figure 17) monitoring on a weekly basis since April 2011 for

ammonium and nitrate (n=121), and weekly measurements of phosphate from

October 2010 to August 2013 (n=107).

6. EWTF effluent (Figure 17) monitoring on a monthly basis since January 2010 for

ammonium (n=65).

Grab samples were collected from eight feet below the water surface near the center of the channel using a peristaltic pump and drill driver; if the water depth did not permit sampling at this depth, samples were collected from four feet below the water surface. Sampling depth was held constant at eight feet below the surface regardless of total water depth because the Bay has been characterized as vertically homogeneous

(Gast and Skeesick, 1964; Casebier and Toimil, 1973). Three liters of sample were collected at each site, pumped directly into clean HDPE or polycarbonate bottles, and placed into an insulated cooler out of sunlight until analysis. Analyses generally took place within 12 hours of sample collection. Chlorophyll-a, DOC, and nutrient samples were frozen between the time of preparation and the time of analysis.

Figure 14 - Sample site map and distances from the mouth of Humboldt Bay.

Figure 15 - Professor Hurst's sample site map and distances from the mouth of Humboldt Bay.

Figure 16 - Wiyot Tribe's sample site map and distances from the mouth of Humboldt Bay.

Figure 17 - Wastewater treatment facility outfall map and distances from the mouth of the Bay.

Sample Analyses

All Bay grab samples were collected, handled, and analyzed using the same methods and equipment. Methodology from Standard Methods for the Examination of

Water and Wastewater were followed for all analyses and instrument calibrations

(APHA, AWWA, WEF, 2012). The same hand held multi-parameter instrument (YSI

556 MPS) was used for field determination of all samples for dissolved oxygen (DO), water temperature, and salinity were determined. Samples were brought back to a laboratory at Humboldt State University where turbidity, pH, and total suspended solids

(TSS) were determined. Turbidity was determined using the Hach 2100Q turbidimeter, pH was measured using an ion-selective probe, and TSS was determined using Whatman

934-AH glass fiber filters. Chlorophyll-a samples were prepared by filtering sample water through 0.7 µm glass fiber filters and then freezing the filters in small plastic vials until the time of analysis. Chlorophyll-a was extracted using acetone and then measured at Humboldt State University's Telonicher Marine Laboratory in Trinidad, California using a Turner Designs Trilogy fluorometer. Nutrient samples and dissolved organic carbon (DOC) samples were prepared by filtering sample water through 0.45 µm polycarbonate track-etched membrane filters. Filtrate was then frozen until analyses were carried out. Nutrient analyses were carried out at Humboldt State University's

Telonicher Marine Laboratory in Trinidad using a Bran+Luebbe Autoanalyzer 3. DOC analyses were carried out at Humboldt State University's BioCore laboratory using a

Shimadzu TOC-L Total Organic Carbon / Nitrogen Analyzer; samples run in the TOC

73 analyzer were filtered prior to analysis, the resulting concentrations thus represented the dissolved component of TOC.

Nutrient samples remained frozen until analyses were conducted, approximately every few months. Frozen samples from each run were saved and re-run during the following analysis to ensure no degradation of nutrients had occurred while frozen.

Standards were also analyzed before and after freezing to ensure freezing had no effects on concentrations. Both of these quality assurance tests indicated no depletion or loss of any nutrient took place during the freezing and storage of samples.

Ammonium-nitrogen was analyzed following the automated phenate method

(Standard Methods: 4500-NH3 G). Nitrite-nitrogen and nitrate-nitrogen were analyzed

- following the automated cadmium reduction method (Standard Methods: 4500-NO3 F).

Orthophosphate-phosphorus was analyzed following the automated ascorbic acid reduction method (Standard Methods: 4500-P F). Silicate-silicon was analyzed following the automated method for molybdate-reactive silica (Standard Methods: 4500-SiO2 E).

Dissolved organic carbon was analyzed following the high-temperature combustion method for total organic carbon (Standard Methods: 5310 B) following filtration of samples with 0.45 µm polycarbonate track-etched membrane filters to remove the particulate component of total organic carbon.

The data sonde deployed on the Indian Island pier collects measurements every 15 minutes using a YSI 6600 EDS multi-instrument sonde. The sonde contains instruments for reading water temperature, water depth, turbidity, salinity, pH, dissolved oxygen, and chlorophyll-a. Chlorophyll-a readings from the sonde are adjusted based upon a

74 correction factor derived from lab measurements of chlorophyll-a in grab samples collected at the same time and location of the sonde. The sonde is also removed and calibrated every two weeks by the Wiyot Tribe Natural Resources Department.

Data Analyses

Two main components make up the nutrient budget, loading from sources, and uptake or storage. Due to the variety of sources for nutrient loading data to Humboldt

Bay, many of the datasets do not overlap in time. Where this is the case, daily, monthly, seasonal, and annual statistics may be used for calculations. Little or no data are available for nutrient removal mechanisms in Humboldt Bay such as phytoplankton production, macroalgae production, eelgrass production, and denitrification, so reference values are used in conjunction with available water quality data and local atmospheric data to estimate this portion of the budget as closely as possible. In order to compile a budget for the whole system, no single nutrient cycling process was explored exhaustively.

For each source or type of uptake, a statistic for sample standard deviation is presented and varies in derivation depending upon the available data. Where multiple years of data are available, the sample standard deviation represents the inter-annual variability in the data. Where data from another system are applied to Humboldt Bay, or literature values are used, the sample standard deviation may represent the sample or measurement variation. Standard deviation statistics are described in more detail in the following sections for each source and type of uptake. Standard deviation statistics are

75 not presented for hydraulic fluxes because the statistics presented for each nutrient source or type of uptake includes variation in the hydraulic flux used to calculate them.

All annual statistics are presented in terms of water years (October through

September). Water years are defined by the calendar year that they end in. For example, water year 2012 (WY 2012) is October 1, 2011 through September 30, 2012. All concentrations are listed in molar and mass concentrations when convenient, different agencies and disciplines may require different concentration units; note that wastewater concentration units are typically reported as mass concentration (e.g. mg/L) whereas typical oceanographic and ecologic concentration units are reported as molar concentration (e.g. mM). Volume is reported in million cubic meters (Mm3), and mass is reported in million grams (Mg), equivalent to a metric ton. The term loading is used to describe the mass input from various sources, and the terms uptake or production are used to denote removal or storage. Geospatial analyses were carried out using ESRI

ArcMap 10.1 and QGIS 2.6.1 in the Universal Transverse Mercator zone 10 (UTM10) coordinate projection. All elevation data are with respect to the North American Vertical

Datum of 1988 (NAVD88).

In order to compare the relative magnitudes of each source and type of uptake, mass loads are calculated using concentration and flow data due to the large difference in flow rates between sources such as wastewater discharge, streamflow, and ocean tides.

This project includes the compilation of flow rate estimations as well as nutrient concentrations for the three major hydraulic components, wastewater, streamflow, and ocean tides, such that mass loading rates (mass per time) can be calculated for direct

76 comparison to one another and allow formation of a mass budget for the system.

Precipitation volumes have also been calculated for comparison of the magnitude of hydraulic inputs to the Bay though precipitation is assumed to have no impact on nutrient loading.

A nutrient mass balance relies on principles of conservation of mass (Equation 3) to account for all sources, sinks, and types of storage. Tracking influx and efflux is much simpler for conservative constituents such as water and salt than it is for nonconservative constituents such as nitrogen, carbon, and phosphorus that are involved in many chemical, physical, and biological transformations (Smith and Hollibaugh, 2006).

Limitations in data availability and computational modeling make a comprehensive nutrient mass balance infeasible, therefore major constituents and processes are estimated using available data to account for significant sources and uptake in the nutrient budget.

A computational model that can simulate water, salt, and temperature fluxes has been constructed for Humboldt Bay (Anderson, 2010) though nutrient cycling has yet to be included.

∑ 푀푎푠푠𝑖푛 − ∑ 푀푎푠푠표푢푡 + ∑ 푀푎푠푠푠푡표푟푎𝑔푒 = 0 (3)

The first step in constructing a mass-based nutrient budget from concentration data requires a water budget quantifying volumes and flow rates. To calculate the mass of any constituent, concentration (mass per volume) is multiplied by flow rate (volume per time) resulting in a mass loading rate (mass per time) that allows comparison of the

77 magnitudes of different sources and uptake. For flow rates entering and leaving

Humboldt Bay, the boundary was set to be the approximate boundary of the water surface at MHHW, and the boundary to the ocean was set as a line crossing the Bay entrance at the outermost points of the north and south jetties.

Humboldt Bay is made up of four morphologically distinct compartments (Arcata

Bay, Main Channel, Entrance Bay, and South Bay) that have been defined here using the approximate MHHW boundary in order to estimate the amount of water and nutrients exchanged between each (Figure 18). Surface areas for each sub-compartment of the Bay were estimated using polygons derived from the USGS WBD vector files that were augmented to fit the water boundary of the active Bay (Table 19). The WBD polygons included salt marshes and wetlands adjoining the Bay that are not considered active parts of the normal tidally influenced surface area.

Figure 18 - Sub-bay boundary map.

Table 19 - Sub-bay and associated watershed surface areas.

Surface Area1 Contributing Watershed Sub-Bay Compartment (Mm2) Area2 (Mm2) Arcata Bay 37 245 Main Channel 6 145 Entrance Bay 8 0 South Bay 18 48 1Anderson (2015); 2WBD (2015)

Tidal Volumes

Flow rates between the ocean and the Bay, and between sub-bays of Humboldt

Bay were generated using a calibrated hydrodynamic circulation model (Anderson,

2015). The model of Humboldt Bay was constructed using the Environmental Fluid

Dynamics Code Explorer (EFDC Explorer) software and calibrated for water surface elevation, salinity, and temperature (Anderson, 2010). Sub-compartment polygons were used to delineate flux boundaries in the model (Figure 19), and flow rates were generated on a 15 minute timestep for the period of 1/1/2012 to 3/31/2015 (example: Figure 20).

Figure 19 - Humboldt Bay EFDC model outline and sub-bay flux line map (Anderson, 2015).

Figure 20 - Example intra-bay flow rates for one tide cycle on January 1, 2012 from EFDC hydrodynamic model (Anderson, 2015); positive values denote flood tide and negative values denote ebb tide.

Watershed Runoff Volumes

Sub-watershed areas were estimated using the USGS National Hydrography

Dataset (NHD) and Watershed Boundary Dataset (WBD) vector file polygons for the

Humboldt Bay watershed. In the cases of Mad River Slough/Liscom Slough, Jacoby

Creek/McDaniel's Slough, and Jolly Giant Creek/Butcher's Slough, the Humboldt Bay

WBD polygon had to be subdivided further to delineate these sub-watersheds as they are not detailed in the original WBD polygon set. These additional sub-watersheds were delineated in order to specify a watershed area for grab samples that were collected at the point of discharge into Humboldt Bay. It should be noted that Mad River Slough is not a typical watershed, it is more of a brackish slough with minimal streamflow and is mostly influenced by tidal flows; however, due to the amount of agricultural lands draining into the slough, it is treated as a typical stream flow for the purposes of this nutrient budget.

Due to lack of direct flow measurements for many freshwater creeks entering

Humboldt Bay, an estimation of runoff flows was made using data from the nearby

USGS streamflow gaging station on Little River (Table 20). The station provides average daily streamflow data (USGS, 2015) that were applied to each sub-watershed of

Humboldt Bay. The Little River watershed is similar in size and location (approximately

6 Nmi north) to the Humboldt Bay sub-watersheds, and should have similar geologic, runoff, and precipitation characteristics. Average daily streamflow for Little River was divided by the area of the watershed to get a flow rate per unit surface area; this value was then multiplied by the surface area of each sub-watershed of Humboldt Bay to get an average daily flow rate for each freshwater stream entering the Bay.

Table 20 - Surface area and streamflow characteristics for each stream entering Humboldt Bay and nearby Little River.

Surface Area1 Minimum2 Average2 Maximum2 Name (Mm2) (m3/s) (m3/s) (m3/s) Little River 116 0.074 2.726 68.244 Mad River Slough 22 0.014 0.509 12.743 Jane's Creek 12 0.008 0.292 7.304 Jolly Giant Creek 5 0.003 0.110 2.750 Jacoby Creek 52 0.033 1.229 30.756 Rocky/Washington Gulches 8 0.005 0.176 4.418 Freshwater Creek 147 0.093 3.453 86.438 Elk River 145 0.092 3.406 85.271 Little Salmon Creek 48 0.030 1.124 28.139 1WBD (2015); 2USGS (2015)

Precipitation Volumes

Average monthly precipitation for the period of record (1886 to 2015) collected by the National Weather Service at Woodley Island in Eureka was applied to the surface area of each sub-bay to estimate hydraulic loads to the Bay from direct precipitation.

While this hydraulic load does not carry any significant nutrient loads, it is included to serve as a point of relative comparison for other hydraulic loads. It should be noted that monthly precipitation during the period of study varied greatly from the historic averages

(0% to 388%); therefore the historic average was used as a point of relative comparison instead of the anomalous (lower) recent values.

Ocean Nutrient Loads

Nutrient measurements collected inside the Entrance Bay within one hour of high tide are considered representative of nearshore waters as the large volume of water entering the Bay during each tide cycle likely replaces much of the volume of the

Entrance Bay. Mass loading to Humboldt Bay and individual compartments from nearshore waters were calculated using the sum of the flood tide volumes (Anderson,

2015), tidal flushing rates for each sub-bay (Anderson, 2010), and nutrient concentrations near the Bay entrance from various datasets (Wiyot Tribe Natural Resources Department,

2015; this study). Flushing rates from Anderson (2010) were provided for Arcata Bay,

Entrance Bay, and South Bay; a flushing rate for the Main Channel was calculated as the volume-weighted average of the Entrance Bay (0.31/tide cycle) and Arcata Bay (0.02/tide cycle) flushing rates since it connects the two (0.14/tide cycle); and a flushing rate for

Humboldt Bay was calculated as a volume-weighted average of all sub-bay flushing rates

(0.12/tide cycle). The sample standard deviation reported for ocean nutrient loading represents inter-annual variability in annual and seasonal loading from two years of nutrient data collected (n = 2).

Wastewater Nutrient Loads

Wastewater loading for the AWTF was calculated from daily flow rate data and weekly nutrient concentration data. Daily nutrient concentrations were linearly interpolated and multiplied by daily flow rates to estimate daily discharge loads for ammonium-nitrogen, nitrate-nitrogen, and orthophosphate-phosphorus. The results of the linear interpolation were then summed on a monthly basis for the period of record

(approximately four years of weekly ammonium and nitrate data collected between April

2011 and May 2015, and nearly three years of weekly phosphate data collected between

October 2010 and August 2013) and used to calculate average monthly and annual loadings to Arcata Bay (City of Arcata, 2015).

Wastewater loading for the EWTF was calculated from monthly ammonium- nitrogen and flow rate data (collected between January 2010 and June 2015), and a single measurement for nitrate-nitrogen and orthophosphate-phosphorus collected on August

31, 2015 (City of Eureka, 2015). This single measurement may not represent the average effluent nitrate or phosphate concentrations of the EWTF, possibly resulting in a significant over or under-estimation. Daily nutrient concentrations and flow rates were linearly interpolated and multiplied to estimate daily discharge loads for ammonium-

85 nitrogen, nitrate-nitrogen, and orthophosphate-phosphorus. The standard deviation reported for wastewater nutrient loading represents inter-annual variability between approximately three years of data (n = 3).

Watershed Nutrient Loads

Watershed loading was calculated using estimated daily inflow rates for each stream based on individual watershed size, scaled by the flow rate at the nearby USGS

Little River stream gaging station (USGS, 2015), and average nutrient concentrations taken from available data (Hurst, 2015 b.). Due to the lack of nutrient data from the surrounding watershed, average nutrient concentrations were applied to the entire watershed and were not varied with time. However, the hydraulic loads do vary with time, increasing and decreasing nutrient loads to the Bay from the watershed in direct proportion to the calculated flow rates. It remains unclear whether nutrient loads vary between sub-watersheds due to differences in land use.

Sixteen samples collected at Freshwater Slough had low enough salinity (below

5.3 ppt) to indicate sufficient freshwater runoff without significant interference from Bay water. These samples were collected between December 2012 and November 2014

(Hurst, 2015 b.). Typical Bay salinity is closer to that of the ocean, approximately 34 ppt, such that selecting for low salinity samples at watershed discharge locations would more accurately indicate the freshwater runoff from the watershed. The standard deviation reported for watershed nutrient loading represents inter-annual variability between approximately two and a half years of data (annual, n = 2; upwelling and runoff

86 seasons, n = 3); data collection began during the upwelling season of 2012 and ended during the runoff season of 2015 such that there are two annual means and three seasonal means.

Phytoplankton Uptake

Phytoplankton carbon uptake rates were calculated using an average between high

(10.9 g C/hr/g Chl-a) and low (1.7 g C/hr/g Chl-a) nutrient assimilation ratios for chlorophyll-a measured by Harding (1973) and Ryther and Yentsch (1957), respectively.

Assimilation rates for nitrogen and phosphorus were determined using the Redfield ratio of 106:16:1 (C:N:P) from Fleming (1940), and silicon uptake rates were determined using a 1:1 (N:Si) uptake ratio for diatoms suggested by Brzezinski (1985). Silicon is included in the phytoplankton uptake estimations to account for any diatom blooms that may occur. Diatoms are only one species of phytoplankton and may not be the dominant species at all times, therefore the application of silicon uptake by diatoms to all phytoplankton uptake calculations likely results in an overestimation of silicon uptake.

Average monthly chlorophyll-a concentrations were calculated for Arcata Bay,

Entrance Bay, South Bay, and the Main Channel using multiple datasets at various locations over a period of many years in some cases. Arcata Bay data include all samples collected from the Mad River Slough, Indian Island, McDaniel's Slough, Indian/Woodley

Island Channel, Arcata Channel, Bird Island, and Mad River Slough Channel sample sites between October 2007 and February 2015 (n = 302). Entrance Bay samples include all data collected at the Bay entrance sample site between October 2007 and February

2015 (n = 76). South Bay data include all samples collected from the Hookton Slough and South Bay sample sites between October 2012 and February 2015 (n = 42). Main

Channel data include all samples collected from the Eureka Channel, Samoa Channel, and Main Channel sample sites between October 2012 and February 2015 (n = 101). All water quality data are listed in Appendix B.

Sample frequency varied from 1-4 times monthly. Average chlorophyll-a concentrations and uptake rates were applied to average monthly volumes of each sub- bay using output from a hydrodynamic model for Humboldt Bay (Anderson, 2015); average monthly volumes approximate the MSL volume of each bay. Note that this assumes complete mixing and homogeneous uptake by chlorophyll-a throughout the water column. This condition is not likely the case since light attenuation in the deeper channels and bays may limit phytoplankton uptake and production, however, a more precise spatial and temporal model of the vertical and horizontal distribution of spectral qualities that occurred is beyond the scope of this project. This assumption may result in an over-estimation of phytoplankton production in the Bay.

The standard deviation reported in phytoplankton production was calculated using the percent relative sample standard deviation from the mean of the two uptake rates proposed by Ryther and Yentsch (1957) and Harding (1973) of 73%. Sample standard deviations were also calculated for the inter-annual variation between the two years of data and ranged from 17-70%; these values were all less than the relative sample standard deviation due to the range in uptake rates, so the latter was used as the more conservative estimate of uncertainty.

Macroalgae Uptake

Macroalgae nutrient uptake in Humboldt Bay was calculated using the areal distribution of macroalgal mats in Humboldt Bay estimated by Schlosser and Eicher

(2012), monthly production rates measured by Pregnall and Rudy (1985), and the stoichiometric ratio of nutrients in macroalgae of 640:42:1 (C:N:P) estimated by Duarte

(1992). Schlosser and Eicher (2012) estimated an areal distribution of macroalgae in

Arcata Bay, Entrance Bay, and South Bay to be 4.18 Mm2, 0.58 Mm2, and 3.96 Mm2, respectively. Pregnall and Rudy (1985) indicated monthly macroalgae production for the months of May through November resulting in a growing season production distribution

(Table 21). Standard deviation reported in macroalgae production was calculated using the percent relative sample standard deviation (% RSD) from the mean reported by

Pregnall and Rudy (1985).

Table 21 - Monthly macroalgae production rates measured in Coos Bay, Oregon; % RSD is the percent of the standard deviation relative to the mean.

Macroalgae Production1 Standard Deviation1 Month (g C/m2) (g C/m2) % RSD May 24.9 20.6 83% June 135.5 81.3 60% July 285.2 131.1 46% August 369.2 193.8 52% September 224.8 70.9 32% October 80.4 33.7 42% November 8.5 3.5 41% 1Pregnall and Rudy (1985)

Eelgrass Uptake

Average monthly eelgrass biomass accumulation measured in Humboldt Bay

(Table 22) by Harding (1973) have been applied to more recent surveys of eelgrass bed distribution in Arcata Bay, South Bay, and Entrance Bay of approximately 14.48 Mm2,

7.88 Mm2, and 0.50 Mm2 respectively, made by Schlosser and Eicher (2012) to calculate current potential eelgrass production in each bay. Using elemental ratios of carbon, nitrogen, and phosphorus of 246:14:1 (C:N:P) measured by Fourqurean et al. (1997) in eelgrasses of Tomales Bay (approximately 200 miles south of Humboldt Bay), monthly and annual eelgrass uptake was calculated for Humboldt Bay. Standard deviation reported in eelgrass production was calculated using the percent relative sample standard deviation from the mean elemental composition by percent of dry weight reported by

Fourqurean et al. (1997) for carbon, nitrogen, and phosphorus (0.6%, 0.07%, and 0.02% respectively). The standard deviation associated with inter-annual variation in spatial distribution and density of eelgrass beds is likely much greater than the standard deviation reported here, though no data on these phenomena could be located for

Humboldt Bay.

Harding (1973) only measured biomass between April and August, representing the majority of the growing season in northern California for eelgrass of April through

September (NMFS, 2014), though Harding's data indicate eelgrass biomass was decreasing during August so biomass accumulation for April through July is assumed to be the total annual biomass increase. Fourqurean et al. (1997) found that elemental ratios in eelgrass varied temporally and spatially, and eelgrass beds can expand and contract

90 significantly in one year such that the estimates of production listed in Table 22 may vary significantly from year to year.

Table 22 - Average monthly eelgrass production rates measured in Arcata Bay and South Bay.

Eelgrass Production1 Month (g C/m2) April 116 May 109 June 209 July 131 August 0 1Harding (1973)

Sediment Flux

Areal sediment flux rates of nitrate, ammonium, phosphate, and silicate measured by Sin et al. (2007) for microalgae covered intertidal mud flats in Yaquina Bay Oregon were applied to the approximate surface area of intertidal mud flats in Humboldt Bay to estimate sediment fluxes. Sin et al. (2007) measured flux rates approximately every other month for one year under both light and dark conditions such that diurnal and seasonal variation in sediment fluxes could be calculated for Humboldt Bay. Months that were not measured by Sin et al. (2007) were linearly interpolated between measurements to generate a monthly set of sediment flux rates for both light and dark periods (Table 23 and Table 24). Values measured by Sin et al. (2007) were multiplied by the average number of light and dark hours per day for each month, and the number of days per month to estimate monthly sediment fluxes for nitrate, ammonium, phosphate, and

91 silicate. Intertidal mud flat surface area in Humboldt Bay was calculated as the difference between MLLW and MHHW surface area of each sub-bay from a hydrodynamic model for Humboldt Bay (Anderson, 2015). Standard deviation reported for seasonal and annual sediment fluxes are with respect to the mean of monthly values reported by Sin et al. (2007).

Nitrate Nitrate Ammonium Ammonium

(µmol/m2/hr) (µmol/m2/hr) (µmol/m2/hr) (µmol/m2/hr) Month Light Dark Light Dark October -20.5 -21.5 -2.5 22.5 November1 -11.0 -22.0 -10.0 45.0 December -10.5 -21.0 -31.0 32.5 January1 -10.0 -20.0 -52.0 20.0 February -15.0 -10.0 -35.2 -52.0 March -20.0 -15.5 -18.4 -27.5 April1 -25.0 -9.0 -1.7 24.6 May -30.5 -26.5 7.5 21.5 June1 -36.0 -44.0 16.7 18.3 July -45.3 -59.0 16.3 49.3 August1 -54.7 -74.0 16.0 80.3 September1 -30.0 -21.0 5.0 0.0 1Sin et al. (2007)

Phosphate Phosphate Silicate Silicate

(µmol/m2/hr) (µmol/m2/hr) (µmol/m2/hr) (µmol/m2/hr) Month Light Dark Light Dark October 0.0 -0.5 -32.5 -14.5 November1 0.0 1.0 -40.0 0.0 December -3.7 6.5 -20.0 141.5 January1 -7.4 12.0 0.0 283.0 February -4.6 -7.4 -8.3 0.0 March -1.8 -6.6 -16.7 -4.1 April1 1.0 -5.8 -25.0 -8.3 May -0.5 -5.0 -59.0 -12.4 June1 -2.0 -4.3 -93.0 -16.6 July -1.3 -3.5 -70.3 -20.7 August1 -0.7 -2.7 -47.7 -24.9 September1 0.0 -1.9 -25.0 -29.0 1Sin et al. (2007)

Denitrification

Denitrification in Humboldt Bay was calculated using an average of the three estimates for Tomales Bay presented by Dollar et al. (1991) and Smith et al. (1991).

Dollar et al. (1991) estimated denitrification in Tomales Bay of between 1.2-1.3 mmol/m2/d (average 1.25 mmol/m2/d) by applying stoichiometric principles of plankton uptake of carbon, nitrogen, and phosphorus through direct measurement of sediment nutrient fluxes. Smith et al. (1991) estimated a denitrification rate of 3.1 mmol/m2/d for

93 the same system at the same time using a whole system nutrient budget technique. Direct measurement of sediment fluxes may result in high or low estimates of whole-system denitrification due to local anomalies (Dollar et al., 1991); the whole-system nutrient budget approach may also contain significant uncertainty due to a lack of direct measurement of fluxes. Therefore an average of the two estimates (1.25 mmol/m2/d and

3.1 mmol/m2/d) is used to estimate denitrification in Humboldt Bay (2.2 mmol/m2/d) using a sample standard deviation of 1.3 mmol/m2/d. The average denitrification rate is applied to the MHHW surface area of Humboldt Bay. Applying both denitrification and sediment nitrate flux may overlap with respect to nitrate uptake by the sediments, though there remains uncertainty as to the source of nitrate for denitrification. The linkage between the two processes of sediment nitrate uptake for algae production and denitrification is organic matter which is not assessed during this analysis; therefore, both processes are included to account for this uncertainty. If nitrate uptake by sediments includes nitrate flux for denitrification, then there will be a partial overlap since sediment flux includes algae uptake. However if denitrification is linked to nitrification of ammonium in sediments and not from the water column, then the two processes are de- coupled via organic matter generation and breakdown such that for the purposes of estimating DIN uptake they are at least partially independent forms of uptake.

RESULTS

The general progression of data presented in the following sections begins with a classification of the two main seasons with respect to dissolved inorganic nutrient concentrations. This is followed by evidence supporting previous conclusions that dissolved inorganic nitrogen (DIN) is the limiting nutrient in Humboldt Bay. Followed by a description of the level of eutrophication in Humboldt Bay with respect to chlorophyll-a and dissolved oxygen concentrations established by the National Estuarine

Eutrophication Assessment (Bricker et al., 1999; Bricker et al., 2003; Bricker et al.,

2007). Then a characterization of processes regulating dissolved inorganic nutrients is examined using data collected at adjacent low and high tides along a longitudinal transect from the Bay entrance to upper Arcata Bay providing evidence for nutrient cycling in

Humboldt Bay. This is followed by a mass quantification of major nutrient sources and uptake, using nutrient concentrations and hydraulic fluxes that are described in detail previously. Finally, the mass budgets of DIN and DIP are presented.

Atmospheric nitrogen fixation and oyster production calculations indicate these are minor contributors to the nutrient budgets so they have been omitted for simplification, although a discussion of potential oyster impacts on phytoplankton populations is included. Nitrite is typically a minor dissolved inorganic nitrogen constituent in marine waters as an intermediate between ammonium and nitrate conversion during nitrification and denitrification (Bianchi, 2013). Nitrite was a minor constituent in most samples (typically less than 10% of nitrate) with the exception of

95 samples where nitrate was depleted. However, nitrite did not exceed 0.6 µM (8.4 µg

N/L) in all Bay entrance samples (n = 111) or 2.1 µM (29.4 µg N/L) in all samples inside the Bay (n = 444). Therefore nitrite is reported as a part of the sum of nitrate and nitrite.

Upwelling Season Response

The upwelling season (April-September) has been previously defined previously with respect to seasonal properties of the Bakun upwelling index near Humboldt Bay, and supported by findings of previous studies discussed in the Review of Literature. The following results support the characterization of the upwelling season in Humboldt Bay with respect to dissolved inorganic nutrient concentrations near the Bay entrance and

Bakun upwelling indices. Average seasonal nutrient concentrations in each sub-bay are also presented to provide a relative characterization of each within the Bay.

Nitrate concentrations as high as 34 µM (0.48 mg N/L) have been measured in upwelled waters off of the Oregon coast (Sigleo et al., 2005) and the highest nitrate concentration measured near the entrance to Humboldt Bay was 26 µM (0.36 mg N/L) on

February 21, 2013 (Wiyot Tribe Natural Resources Department, 2015). Average upwelling season nitrate concentrations were significantly higher near the Bay entrance than inside the Bay as a result of upwelled nutrients in nearshore waters and significant uptake of nutrients inside Humboldt Bay (Figure 21 and Figure 22).

Silicate concentrations were significantly higher in Arcata Bay and South Bay than near the Bay entrance with the highest average silicate concentrations occurring in

South Bay (Figure 21). Since there are no wastewater inputs in South Bay, higher silicate

96 concentrations may be attributable to natural variation in watershed geology and not to wastewater discharge. Greater silicate concentrations inside Humboldt Bay compared with nearshore concentrations indicates there is a significant internal source of silicate in the system. This source may be mineralization of silicate in sediments from accumulated watershed runoff particulate matter or diatoms from nearshore production, although the actual source of this silicate is not clear from data presented in this study. Silicate concentrations decreased near the Bay entrance during the upwelling season due to diatom production in nearshore waters (Figure 23). However, early season upwelling events indicate that upwelling is a significant source of silicate to the Bay when production is low. Silicate and nitrate show a similar seasonal pattern of decreasing significantly during the upwelling season near the Bay entrance as diatoms uptake nitrate and silicate in a 1:1 stoichiometric ratio (Figure 22 and Figure 23). This indicates that diatoms are a major phytoplankton species influencing nutrient uptake in nearshore waters and Humboldt Bay.

Ammonium concentrations are much lower than silicate and nitrate concentrations in nearshore waters and increase less during upwelling events (Figure 24).

Ammonium uptake by phytoplankton during the upwelling season is also significantly less than nitrate and silicate, though this may be complicated by re-mineralization of ammonium from phytoplankton biomass following uptake of nitrate from upwelling.

Ammonium concentrations were also greater inside Arcata Bay compared with South

Bay and nearshore waters (Figure 21) indicating a significant source of ammonium exists

97 in Arcata Bay. This source is likely from re-mineralization of accumulated material in

Arcata Bay as opposed to freshwater sources as will be discussed later.

Phosphate concentrations are lower than silicate, nitrate, and ammonium in nearshore waters, although phosphate also shows signs of increasing during non- productive season upwelling events and being assimilated by phytoplankton during the productive part of the upwelling season (Figure 25). Phosphate is assimilated by phytoplankton at a much lower ratio with nitrogen, which explains the relatively low decrease in phosphate concentrations during the productive upwelling season compared with nitrate. Greater concentrations of phosphate were also measured in Arcata Bay than in South Bay or nearshore waters (Figure 21), although as mentioned previously with respect to ammonium, this source is likely from re-mineralization of accumulated material in the Bay and not from freshwater sources as will be discussed later.

Figure 21 - Average upwelling season nutrient concentrations in each sub-bay between 2007 and 2015 (Hurst, 2009; Wiyot Tribe Natural Resources Department, 2015; this study).

Figure 25 - Average monthly high tide phosphate concentrations at the Bay entrance and Bakun upwelling indices (Wiyot Tribe Natural Resources Department, 2015; this study; PFEL, 2015).

100

Runoff Season Response

The runoff season (October-March) has been previously defined with respect to seasonal properties of precipitation in Humboldt Bay. The following results support the characterization of the runoff season in Humboldt Bay with respect to dissolved inorganic nutrient concentrations at Mad River Slough and total monthly precipitation at Woodley

Island. Average seasonal nutrient concentrations in each sub-bay are also presented to provide a relative characterization of each within the Bay.

Average runoff season nitrate concentrations are significantly higher in Arcata

Bay, the Main Channel, and South Bay compared with the upwelling season as biological productivity decreases (Figure 26). Nitrate concentrations are higher near the Bay entrance during the runoff season indicating nearshore waters still contain significant amounts of nitrate compared with waters inside the Bay. Waters in Mad River Slough increase in nitrate concentration following precipitation events indicating that watershed runoff may contribute significantly more nitrate during the runoff season than during the upwelling season (Figure 27).

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Figure 26 - Average seasonal nitrate concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study).

102

Average runoff season ammonium concentrations are greater in Arcata Bay and

South Bay compared with upwelling season concentrations due to decreased biological productivity (Figure 28). Higher ammonium concentrations in Arcata Bay, South Bay, and the Main Channel are due to re-mineralization of accumulated organic matter and not necessarily the direct result of freshwater discharge as will be discussed later.

Ammonium concentrations show an opposite trend with distance from the Bay entrance compared with nitrate (Figure 26 and Figure 28, respectively). This is due to nitrate being the major DIN constituent in nearshore waters and ammonium increasing in significance inside the Bay due to uptake of nitrate and re-mineralization of accumulated organic matter producing ammonium. Waters near Mad River Slough also indicate that ammonium concentrations increase following precipitation and runoff events indicating ammonium discharge from watershed runoff may increase significantly during the runoff season (Figure 29).

103

Figure 28 - Average seasonal ammonium concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study).

104

Average seasonal silicate concentrations in Humboldt Bay increase with distance from the Bay entrance, with the greatest concentrations occurring during the runoff season and in South Bay (Figure 30). During the upwelling season, lower silicate concentrations in nearshore waters compared with those inside the Bay are due to diatom production. During the runoff season, higher silicate concentrations inside the Bay are due to mineralization of particulate matter. Sediment loads from the watershed may contain significant amounts of siliceous particulate matter, although the relative contribution of this source compared to diatomaceous material accumulated during the productive upwelling season is not clear from data collected during this study. Silicate concentrations in Mad River Slough generally increase following precipitation events

(Figure 31), indicating that watershed contributions of dissolved silicate may be significant; although as mentioned previously, there may be significant amounts of siliceous material contained in watershed sediment loads as well.

2014 was an exceptional year with below average precipitation and high silicate concentrations at Mad River Slough during the upwelling season (Figure 31). This is in contrast to the two other years of data that indicate a clear relationship of increased runoff and silicate exists. Mad River Slough does not necessarily represent a typical watershed input to Humboldt Bay as it is largely tidally influenced and collects drainage from a large flat area of agricultural pastureland. However, this site has one of the longest and most continuous nutrient datasets for a watershed runoff site in Humboldt Bay.

Insufficient data exist to determine seasonal patterns of DIN, phosphate, and silicate from freshwater runoff sources to Humboldt Bay as all of the samples from Mad River Slough

105 had salinity greater than or equal to 20 ppt. The cause of the increased silicate concentrations in Mad River Slough during the upwelling season of 2014 is not clear.

Figure 30 - Average seasonal silicate concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study).

106

Average seasonal phosphate concentrations increased with distance from the Bay entrance into Arcata Bay and were similar in South Bay and the Bay entrance, indicating that there is a source of phosphate in Arcata Bay (Figure 32). Phosphate concentrations were lower throughout the Bay during the runoff season indicating that an increased supply from upwelling in nearshore waters and higher re-mineralization as temperatures increase play an important role in generating phosphate in the system. As will be discussed later, phosphate loads from freshwater sources decrease significantly during the upwelling season. Mad River Slough phosphate concentrations decreased significantly during the runoff season indicating that watershed runoff is a minor contributor of phosphate to the system (Figure 33). Increasing phosphate concentrations in Mad River

Slough during the upwelling season indicates decomposition and re-mineralization of organic matter may significantly increase watershed phosphate contributions during the upwelling season. However, this does not take into account lower watershed runoff flow rates during the upwelling season that may counteract increasing concentrations to moderate the seasonal changes in mass discharge.

107

Figure 32 - Average seasonal phosphate concentrations in Humboldt Bay measured between 2007 and 2015 (Hurst, 2009; Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study).

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Nitrogen Limitation

Seasonal nitrogen limitation in Humboldt Bay has been determined by Pequegnat and Butler (1981) using bioassay tests, and is supported by more recent observations by

Martin and Hurst (2008). Nitrogen is typically the limiting nutrient in healthy estuarine and coastal waters (Bricker et al., 2007). Stoichiometric nitrogen to phosphorus ratios

(N:P) in Humboldt Bay provide additional support for the limiting role of nitrogen

(Figure 34). The N:P ratio in upwelled ocean water is approximately 15:1, similar to the stoichiometric ratio found in phytoplankton biomass of 16:1 (Fleming, 1940). This famous ratio is called the "Redfield Ratio" after Redfield (1934) who first proposed the stoichiometric relationship of nitrogen to phosphorus in phytoplankton, although he initially proposed a ratio of 20:1. Fleming (1940) later modified this relationship using a wider collection of measurements. Due to the similarity between the natural N:P ratio in upwelled seawater and the stoichiometric composition of phytoplankton, as phytoplankton assimilate DIN and phosphate, the relative concentration in the water should remain the same. An N:P ratio below 16:1 indicates DIN will be limiting to phytoplankton production (Ryther and Yentsch, 1957). While phytoplankton will assimilate ammonium before nitrate (Dortch et al., 1982), ammonium is generally a minor constituent in nearshore waters compared with nitrate (Figure 35).

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110

Eutrophication Level

Data from estuaries throughout the United States used for the National Estuarine

Eutrophication Assessment by the National Oceanic and Atmospheric Administration classify systems with typical chlorophyll-a concentrations between 0-5 µg/L and 5-20

µg/L as low and medium eutrophication respectively (Bricker et al. 1999; Bricker et al.,

2003; Bricker et al. 2007). An average of maximum annual chlorophyll-a concentrations in Humboldt Bay measured during WY 2013 and WY 2014 (Figure 36) indicate the system is in the medium range of eutrophication during the upwelling season (Table 25).

The Entrance bay, Main Channel, and South Bay remain in the low eutrophication range during the runoff season, while Arcata Bay is in the medium eutrophication range year- round. Maximum chlorophyll-a concentrations were measured in the Main Channel indicating phytoplankton blooms from nearshore waters increase productivity inside the

Bay at times. Lower concentrations in Arcata Bay than the Main Channel indicate that nutrient limitation and grazing may play significant roles in reducing phytoplankton populations in Arcata Bay. The highest chlorophyll-a concentrations measured in

Humboldt Bay of 20 µg/L occurred in the Main Channel on April 26, 2013 and June 21,

2013.

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Eutrophication Status Maximum Chlorophyll-a Low 0-5 µg/L Medium 5-20 µg/L High 20-60 µg/L Hyper-eutrophic > 60 µg/L

A second eutrophication classification developed by the National Estuarine

Eutrophication Assessment uses bottom water dissolved oxygen (Bricker et al. 1999;

Bricker et al., 2003; Bricker et al. 2007). This classification indicates that Humboldt Bay exhibits biologically stressful concentrations of dissolved oxygen in the Main Channel

112 during the upwelling season, although the rest of the Bay remains healthy with respect to this classification (Figure 37). Note that this classification system uses bottom water dissolved oxygen as the indicator (Table 26) whereas dissolved oxygen concentrations measured in Humboldt Bay represent water column measurements and may not be directly comparable. Bottom water and water column values may vary significantly due to sunlight availability, water depth, vegetative cover, and biological activity occurring at the sediment water interface. The relationship between bottom water and water column dissolved oxygen in Humboldt Bay has not been documented.

Figure 37 - Minimum dissolved oxygen concentrations in Humboldt Bay measured during WY 2013 and WY 2014 (Hurst 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study).

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Minimum Bottom Water Eutrophication Status Dissolved Oxygen Anoxic 0 mg/L Hypoxic 0-2 mg/L Biologically Stressful 2-5 mg/L

Climatic Anomalies

Upwelling and runoff seasons are typical, based on decades of atmospheric data, and can vary significantly from year to year. Extreme variations in climatic conditions can result in abnormal environmental conditions of nutrient loading and biological production. Annual precipitation was below normal for all four of the water years when nutrient data were collected in Humboldt Bay (Table 27). Low precipitation translates to reduced runoff and potentially fewer nutrients entering Humboldt Bay from the surrounding watershed.

Solar insolation is another important environmental factor influencing productivity in Humboldt Bay. As a coastal region in northern California, Humboldt Bay can experience cool foggy summers and cool wet winters. While solar insolation data for the Humboldt Bay region only dates back to May 2007 (SoRMS, 2015), WY 2014 was approximately 140% of the annual average insolation with significantly higher insolation occurring during the winter of 2013-2014 (Figure 38). Increased solar insolation during

WY 2014 may have resulted in increased biological nutrient uptake.

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Table 27 - Total annual precipitation at Woodley Island during the sampling period was between 50-84% of the average for the period of record.

Water Year Total Annual Percent of Average (Oct-Sept) Precipitation1 (in) for Period of Record 1886-2014 39.5 (average) 100% 2008 33.1 84% 2009 30.3 77% 2013 32.0 81% 2014 19.8 50% 2015 (Oct-Feb) 24.8 91% 1WRCC (2015)

Figure 38 - Total monthly direct normal solar insolation for water years 2008, 2009, 2013, and 2014 (SoRMS, 2015).

Intertidal Properties

Samples collected along a longitudinal transect from the Bay entrance to Arcata

Bay during adjoining high and low tides provides evidence for temporal and spatial

115 distribution of nutrient sources and uptake. Temperature and salinity affect water density that may change the mixing properties of the Bay with nearshore currents. The extent to which Bay waters mix with nearshore currents is not well understood and likely varies seasonally as nearshore and inner Bay conditions change. Spatial and intertidal temperature gradients in the Bay are greatest during the summer as sunlight and warm air temperatures heat water flowing over the shallow intertidal mud flats (Figure 39). Note that Figure 39 shows the location of samples collected along the longitudinal transect analyzed throughout the following section. Salinity gradients between the Bay entrance and Arcata Bay are greatest during the winter when increased precipitation and runoff results in increased dilution (Figure 40). Nearshore waters near the Bay entrance are also lower in salinity during the runoff season due to dilution of nearshore currents flowing northward from the Eel River approximately eight miles to the south of the mouth of

Humboldt Bay. The mouth of the Mad River 15 miles to the north may also influence conditions at the Bay entrance when nearshore currents flow southward in the summer.

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Figure 39 - Longitudinal and intertidal temperature gradients are greatest during the summer as water is heated over the shallow intertidal mud flats at low tide.

Figure 40 - Longitudinal and intertidal salinity gradients are greatest during the runoff season as freshwater runoff dilutes Arcata Bay.

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Chlorophyll-a

Chlorophyll-a concentrations measured using an in-situ data sonde at Indian

Island typically peak at high tides and reach minima at low tides (Figure 41). Continuous measurements at Indian Island represent the water that moves between Arcata Bay and the Main Channel as these two bodies may not be completely mixed. During ebbing tides, water from Arcata Bay is moving into the Main Channel. Decreasing chlorophyll-a concentrations during these periods indicates lower phytoplankton populations exist inside the Bay. Grazing of phytoplankton by filter-feeding shellfish and zooplankton

(Cloern, 1991), and reduced production due to nutrient limitation may significantly reduce phytoplankton populations in Arcata Bay, although the relative extent to which these processes contribute to reducing phytoplankton populations is not clear.

A carrying capacity analysis was completed for the recent proposed expansion of shellfish mariculture in Arcata Bay and concluded that even with a twelve-fold increase in shellfish production, phytoplankton food sources would not be significantly affected

(H.T. Harvey & Associates, 2015). This study suggested that while farmed shellfish may filter large volumes of water and remove a significant amount of phytoplankton, the high turnover rate of phytoplankton (doubling more than two times per day) would more than account for removal by farmed filter feeders. This study did not account for grazing by native shellfish populations and zooplankton such that the extent to which grazing actually occurs in Arcata Bay is not clear. The dynamics of phytoplankton reproduction and consumption by filter feeders is not directly addressed in this analysis, however the export of oysters from Arcata Bay has been estimated to be minor compared with other

118 types of uptake (approximately 0.05% of DIN uptake, and 0.04% of phosphate uptake annually in Arcata Bay).

During the upwelling season of 2014, phytoplankton production increased in nearshore waters with higher chlorophyll-a concentrations occurring near the Bay entrance during high tide, and significantly lower production occurring inside the Bay at low tide (Figure 42). This is a strong indication that phytoplankton production begins in nearshore waters and decreases once inside the Bay. The combination of upwelled nutrients and increased sunlight during the upwelling season resulted in increased phytoplankton production, though concentrations inside the Bay remained low (less than

5 µg/L) with respect to eutrophication metrics established by Bricker et al. (2003).

During the non-upwelling/runoff season of October through March, phytoplankton production remained low throughout the Bay and in nearshore waters due to reduced nutrient and sunlight availability.

119

Figure 42 - High and low tide chlorophyll-a concentrations along a longitudinal transect from the Bay entrance to Arcata Bay.

120

Nitrate

Increased phytoplankton production in June 2014 (Figure 42) followed an early season upwelling event in March 2014, indicated by increased nitrate concentrations near the Bay entrance at high tide (Figure 43). As phytoplankton production increased in June

2014 (Figure 42), nitrate concentrations near the Bay entrance decreased due to assimilation by phytoplankton (Figure 43). Upwelling conditions were observed again on

June 16, 2014, indicated by elevated nitrate concentrations near the Bay entrance and into the Main Channel (Figure 43). Elevated levels of nitrate in the Entrance Bay and Main

Channel coincide with high chlorophyll-a concentrations (Figure 42) indicating nitrate was in excess of phytoplankton demand in nearshore waters. High productivity of phytoplankton, eelgrass, macroalgae, and denitrification inside Arcata Bay during this time resulted in low nitrate concentrations at low tide. Limited exchange between the

Entrance Bay, Main Channel, and Arcata Bay increase residence times in each compartment and may play a significant role in lower nitrate concentrations as more time is allowed for uptake and removal. Low nitrate concentrations in Arcata Bay at low tide are also a strong indicator that freshwater sources have little or no impact on ambient nitrate concentrations in the Bay.

During the low runoff season of January 2014, low nitrate concentrations inside

Arcata Bay compared with the Bay entrance may be attributed to denitrification, as production and assimilation would have been minimal at this time. This study did not determine nitrate-specific uptake by various processes as no data are available for denitrification or uptake of nitrate in Humboldt Bay. However, the mass of nitrate-

121 nitrogen removed annually and seasonally via denitrification is estimated using literature values from a similar system and is reported in later sections.

The runoff season including January 2014 resulted in below-average precipitation, while the following runoff season including February 2015 saw above-normal precipitation. These phenomena may explain why nitrate concentrations decreased with distance from the Bay entrance in January 2014, while in February 2015 nitrate concentrations increased with distance from the Bay entrance (Figure 43). Lower runoff in January 2014 may have reduced the watershed runoff nitrate load to the Bay, resulting in lower nitrate concentrations compared with normal runoff conditions the following year. On October 12, 2014 nitrate concentrations increased with distance from the Bay entrance following 2.5 inches of rainfall on September 24, 2014. This evidence indicates that freshwater sources may have a significant impact on nitrate concentrations in Arcata

Bay during the runoff season.

The Average AWTF nitrate discharge during the runoff season is approximately

1.6 Mg nitrate-N whereas watershed runoff contributes approximately 34 Mg nitrate-N indicating that watershed runoff is the major freshwater contributor of nitrate to Arcata

Bay during the runoff season and not the AWTF. An average runoff season watershed discharge to Arcata Bay is approximately 0.766 Mm3/d and the average watershed nitrate concentration used in this analysis is 17.7 µM (248 µg N/L). Applying these values to the MSL volume of Arcata Bay results in a potential nitrate concentration increase of

0.35 µM (4.9 µg N/L) during a typical runoff season day. The average runoff season ambient nitrate concentration in Arcata Bay is 9.1 µM (127 µg N/L) indicating watershed

122 runoff may account for less than 4% of the nitrate in Arcata Bay on a single day. Arcata

Bay does not completely flush during a single day so nutrients may accumulate in the

Bay over a longer period. This is also complicated by the fact that uptake of nutrients in the Bay may provide temporary storage and periodic release. These calculations are intended to serve as a comparison of the relative magnitude of nutrient inputs to the Bay with respect to the volume and ambient concentrations in the Bay.

123

Figure 43 - High and low tide nitrate concentrations along a longitudinal transect from the Bay entrance to Arcata Bay.

124

Silicate

In July and August 2014, silicate concentrations at the Bay entrance fell to below limiting concentrations for diatom production of 2 µM (28 µg N/L; Fisher et al., 1992;

Figure 44), indicating the phytoplankton bloom in nearshore waters (indicated by an increase in chlorophyll-a, Figure 42) may have been predominantly diatomaceous.

During this period nitrate was similarly low (below the 2 µM limiting concentration) at high tide indicating that both could have been limiting factors to nearshore phytoplankton production. However, inside Arcata Bay only silicate was elevated while nitrate remained low throughout, indicating nitrate was the limiting nutrient inside the Bay.

Nitrate may be assimilated by various types of aquatic vegetation inside the Bay and is also removed via denitrification, whereas silicate is not significantly impacted by either of these processes. This is likely the reason why nitrate concentrations decrease in the

Bay while silicate concentrations remain elevated.

During the low runoff season experienced in January 2014, silicate concentrations were approximately equal throughout Bay and during both tides, whereas during the following normal runoff season of 2014-2015, silicate concentrations increased with distance from the Bay entrance and at low tide. This indicates that during the runoff season silicate concentrations in the Bay increase due to watershed runoff. Applying the average watershed runoff silicate concentration used in this analysis of 127 µM (1.78 mg

Si/L) and the average runoff season daily watershed inflow to Arcata Bay of 0.766

Mm3/d to the MSL volume of the Bay results in a potential increase in silicate concentration of 2.5 µM (71 µg Si/L). The ambient water column silicate concentration

125 in Arcata Bay during the runoff season is 29.3 µM (256 µg Si/L) indicating that watershed runoff may account for 9% of the daily silicate in in the Bay. Note that this calculation does not account for reduced tidal exchange and biological cycling that may significantly increase or decrease the actual impact of inputs on ambient concentrations in the Bay.

126

Figure 44 - High and low tide silicate concentrations along a longitudinal transect from the Bay entrance to Arcata Bay.

127

Ammonium

Ammonium concentrations generally increased with distance from the Bay entrance and were higher at low tides indicating a significant internal source exists

(Figure 45). Ammonium discharge from the AWTF decreases significantly during the summer due to plant uptake in the natural treatment system (average ammonium concentration decreases from 237 mM, 16.9 mg N/L, to 85 mM, 6.1 mg N/L, respectively). Applying these concentrations to the average daily discharge from the

AWTF results in potential daily increases in ammonium concentration in the MSL volume of Arcata Bay of 0.3 µM (3.7 µg N/L) during the runoff season and 0.1 µM (1.1

µg N/L) during the upwelling season. The average ammonium concentration in Arcata

Bay during the runoff season was 6.8 µM (95 µg N/L) and during the upwelling season was 5.8 µM (80.6 µg N/L), indicating that the AWTF discharge may account for approximately 4% and 1% of the daily ammonium in Arcata Bay during the runoff and upwelling seasons respectively.

Ammonium concentrations throughout the Bay remained above limiting concentrations for phytoplankton production (2 µM, 28 µg N/L; Fisher et al., 1988) all year with the exception of February 1, 2015 at high tide. However, phytoplankton production will decrease at concentrations up to 5 µM (Hurst, 2015 a.), while 2 µM is the concentration where phytoplankton production essentially ceases completely. Minimum ammonium concentrations in Arcata Bay during the upwelling and runoff seasons of

2014 were 3.4 µM and 1.1 µM, respectively (47.6 µg N/L and 15.4 µg N/L, respectively) with averages of 6.8 µM and 7.1 µM, respectively (95.2 µg N/L and 99.5 µg N/L,

128 respectively). Marine plants typically assimilate ammonium preferentially to nitrate at ammonium concentrations above 0.5 µM (7 µg N/L; Eppley et al., 1969; Strickland et al.,

1969) indicating that ammonium plays a significant role in limiting production in the

Bay.

129

Figure 45 - High and low tide ammonium concentrations along a longitudinal transect from the Bay entrance to Arcata Bay.

130

Phosphate

Phosphate concentrations inside Arcata Bay remained in excess of metabolic requirements for phytoplankton production at all times (0.2 µM, 6.2 µg P/L; Fisher et al.,

1992) with the exception of the July 2014 diatom bloom near the Bay entrance and in the

Main Channel (Figure 46). Phosphate concentrations generally increased with distance from the Bay entrance and at low tides during the upwelling season (April-September), indicating a high degree of uptake near the Bay entrance and contribution of internal sources in the Bay.

Following the low runoff season including January and March 2014, phosphate concentrations decreased slightly with distance from the Bay entrance (Figure 46), whereas during the normal runoff season of 2014-2015, concentrations increased with distance from the Bay entrance. This indicates freshwater sources may increase phosphate concentrations in the Bay during the runoff season. However, as mentioned previously, phosphate concentrations decreased at Mad River Slough and Freshwater

Slough with increasing precipitation suggesting wastewater from the AWTF may influence phosphate concentrations in Arcata Bay during the runoff season. On

December 30, 2014 concentrations were higher at high tide than at low tide between the

Bay entrance and Arcata Bay, although it should be noted that this is the only sample where there was a single tide cycle between low tide and high tide samples. The low tide sample was collected on December 30th in the afternoon, and the high tide sample was collected on December 31st in the morning, although it is unclear whether this caused the difference in phosphate concentrations.

131

Figure 46 - High and low tide phosphate concentrations along a longitudinal transect from the Bay entrance to Arcata Bay.

132

Nutrient Sources

Major dissolved inorganic nutrient inputs to Humboldt Bay include ocean influx, wastewater discharge, watershed runoff, and sediment flux. It should be noted that other major sources of nutrient inputs to bays and estuaries not considered here include particulate organic and inorganic matter, and dissolved organic matter. These nutrient forms can be a source of dissolved inorganic nutrients as material decays and dissolved inorganic nutrients are mineralized. Also note that sediment flux estimates use values from another similar estuarine system on the Oregon coast applied to Humboldt Bay.

Ocean Influx

Average seasonal dissolved inorganic nutrient loading to Humboldt Bay increases by between 4-40% during the upwelling season compared to the runoff season due to nutrient rich upwelled ocean water (Table 28). Chlorophyll-a production increases by approximately 290% on average during the upwelling season as nearshore phytoplankton production is stimulated by the upwelled nutrients and increased sunlight availability.

During the upwelling season, DIN loading increases by approximately 20% (ammonium by 40% and nitrate + nitrite by 15%), phosphate increases by approximately 12%, and silicate-Si increases by approximately 4%.

133

Table 28 - Average annual and seasonal chlorophyll-a and nutrient loading to Humboldt Bay (and standard deviations).

Upwelling Season Runoff Season Constituent (Apr-Sep) (Oct-Mar) Annual 188 48 237 Chlorophyll-a1 (Mg) (± 28) (± 8) (± 36) 6,151 5,329 11,480 Nitrate + Nitrite1 (Mg N) (± 1,298) (± 1,008) (± 291) 1,682 1,202 2,883 Ammonium1 (Mg N) (± 152) (± 217) (± 369) 1,404 1,250 2,653 Phosphate1 (Mg P) (± 440) (± 249) (± 191) 16,860 16,138 32,998 Silicate1 (Mg Si) (± 3,964) (± 776) (± 3,188) 1This study, Wiyot Tribe Natural Resources Department (2015)

Wastewater Discharge

Nutrient data from the AWTF have been made available by the City of Arcata for the purposes of this study (City of Arcata, 2015). Ammonium and nitrate measurements have been collected on a weekly basis since April 2011, and phosphate concentrations were collected on a weekly basis between October 2010 and August 2013. Ammonium is the most significant source of DIN from the AWTF during the high discharge runoff season (Figure 47). Seasonal fluctuations in ammonium, nitrate, and phosphate concentrations from the AWTF are due, in part, to fluctuations in flow rates resulting from increased influent to the facility, and direct rainfall on the approximately 90 acres of ponds and wetlands (Figure 48). Multiplying the nutrient concentration by the flow rate to get a mass discharge rate significantly alters the apparent discharge of nutrients from the treatment facility, especially with respect to phosphate (Figure 49). Phosphate concentrations increase during the summer when flow rates are lower (Figure 47),

134 however, the mass discharge of phosphate from the facility increases during the winter as biological activity slows and decomposition of organic matter releases phosphate into the water column (Figure 49). Since ammonium and nitrate concentrations increase during the winter due to reduced biological uptake and storage, the seasonal pattern of higher discharge concentration and mass remains the same for these constituents.

Figure 47 - AWTF effluent ammonium, nitrate, and phosphate concentrations between April 2011 and April 2015 (City of Arcata, 2015); note wastewater concentrations are typically reported as mg/L.

135

Figure 49 - AWTF effluent ammonium, nitrate, and phosphate mass loads between April 2011 and April 2015 (City of Arcata, 2015); note Mg refers to million grams, equivalent to one metric ton.

136

Monthly ammonium concentrations and flow rates were made available for the

EWTF by the City of Eureka dating back to January 2010, and a single measurement of nitrate and orthophosphate was collected on August 31, 2015 (City of Eureka, 2015).

The EWTF utilizes a more conventional treatment system resulting in less seasonal variation than the AWTF (Figure 50). Eureka's system includes a nitrifying trickling filter that converts ammonium to nitrate, which explains why the EWTF effluent ammonium is lower and nitrate is higher than the AWTF, even though the AWTF has a lower average inflow rate (Table 29). Seasonal fluctuation in effluent flow from the

EWTF is also much less than the AWTF due to much less open surface wetland and pond area for collecting precipitation. Less variation in the effluent flow rate also results in the same pattern of discharge concentration and mass load (Figure 50).

137

Table 29 - Nutrient concentration and loading ranges (and means) for the AWTF and EWTF; only one value for nitrate and phosphate were collected for EWTF effluent on August 31, 2015.

Wastewater Treatment Facility Units Phosphate-P Nitrate-N Ammonium-N 0.07 - 0.25 0.01 - 0.31 0.01 - 2.68 AWTF1 mM (0.15) (0.06) (0.75) 2.1 - 7.8 0.2 - 4.3 0.2 - 37.5 AWTF1 mg/L (4.6) (0.9) (10.5) 0 - 0.12 0 - 0.06 0 - 0.62 AWTF1 Mg/d (0.03) (0.01) (0.09) 0.01 - 0.93 EWTF2 mM 0.31 1.06 (0.12) 0.1 - 13.0 EWTF2 mg/L 9.7 14.9 (2.5) 0.10 - 0.36 0.15 - 0.55 0 - 0.21 EWTF2 Mg/d (0.17) (0.26) (0.04) 1City of Arcata, 2015; 2City of Eureka, 2015

The potential increase in nitrogen concentration of Arcata Bay due to wastewater discharge from the AWTF and EWTF estimated by Pequegnat and Butler (1981) of 0.5

µM (7.0 µg N/L), is an order of magnitude greater than what is now the case given current conditions. Wastewater loading implied by Pequegnat and Butler (1981) was between 0.34-0.60 Mg N/d and is comparable to the current combined average annual

DIN discharge of 0.403 Mg N/d load from the AWTF and EWTF. However, since the

EWTF does not discharge to Arcata Bay, a more accurate estimation of this calculation using the average DIN discharge load from the AWTF of 0.09 Mg N/d (City of Arcata,

2015) and a MHW volume of approximately 66.9 Mm3 (Anderson, 2015), results in a

0.10 µM (1.35 µg N/L) potential increase in the concentration of Arcata Bay. This calculation was strictly done for comparison to previous methods. This assumes the Bay

138 is completely mixed, does not account for any of the numerous processes involved in nitrogen cycling in the Bay. Discussion of the comparative magnitude of the wastewater

DIN load to Arcata Bay with other sources and types of uptake will be discussed in a later section.

The EWTF discharges directly into the Main Channel near the Bay entrance on outgoing tides only such that their nutrient load may have a minimal impact on Arcata

Bay and South Bay. The MHHW-MLLW tidal prism in the Main Channel is approximately 11 Mm3 whereas the MLLW volume of the Entrance Bay is approximately

40 Mm3 indicating the EWTF discharge may not completely exit the Bay before the tide reverses direction. DIN loading from the EWTF is primarily in the form of nitrate-N as their system utilizes a nitrifying trickling filter that converts much of the ammonium to nitrate. The EWTF only discharges on outgoing tides such that any measureable effects of their discharge on waters near the Coast Guard sample station and Bay entrance sample station would be detectable near low tide. Of the 12 low tide samples collected at these locations, there is no discernable pattern of elevated nitrate levels from the EWTF discharge. The maximum discharge from the EWTF is approximately 0.04 Mm3/d (9.8

MGD), nitrate-N measured in their effluent was approximately 1.1 mM (15 mg N/L), the average flow rate from the Main Channel to the Entrance Bay is 242 Mm3/d (63,930

MGD) resulting in a possible increase in concentration of the main channel flow of approximately 0.16 µM (2.3 µg N/L) assuming complete mixing. An increase in nitrate concentration of this magnitude would be virtually impossible to attribute to the EWTF discharge apart from other possible causes.

139

Annual ammonium and nitrate mass discharges from the AWTF and EWTF indicate that the AWTF is a much more significant source of ammonium while the EWTF is potentially a more significant source of nitrate (Table 30 and Table 31). It should be noted that the calculation of nitrate-N discharged from the EWTF is based upon a single measurement of nitrate-N concentration and the actual annual average may vary significantly from the measured value (Table 31). The AWTF utilizes a natural constructed wetland treatment system that exhibits significant seasonal variability of ammonium discharge increasing approximately 335% during the runoff season as the vegetation in the system senesces, decreasing DIN uptake and releasing nitrogen stored in decaying biomass through re-mineralization (Table 30). The average annual hydraulic discharge from the EWTF is over two times the average annual hydraulic discharge from the AWTF, and the estimated phosphate discharge from the EWTF (based on a single phosphate sample) is over four times that of the AWTF.

Table 30 - AWTF annual and seasonal hydraulic and nutrient loading to Humboldt Bay (and standard deviations).

Upwelling Season Runoff Season Constituent (Apr-Sep) (Oct-Mar) Annual Discharge1 (Mm3) 0.98 (± 0.25) 1.61 (± 0.34) 2.58 (± 0.62) Nitrate1 (Mg N) 0.81 (± 0.07) 1.64 (± 0.56) 2.44 (± 0.59) Ammonium1 (Mg N) 6.98 (± 5.17) 30.39 (± 8.59) 37.38 (± 14.91) Phosphate1 (Mg P) 4.65 (± 0.55) 8.55 (± 1.76) 13.19 (± 2.21) 1City of Arcata, 2015

140

Upwelling Season Runoff Season Constituent (Apr-Sep) (Oct-Mar) Annual Discharge1 (Mm3) 2.94 (± 0.49) 3.36 (± 0.54) 6.30 (± 0.66) Nitrate1 (Mg N) 43.80 (± 7.31) 50.15 (± 8.04) 93.95 (± 9.84) Ammonium1 (Mg N) 8.80 (± 3.46) 6.04 (± 4.12) 14.85 (± 4.19) Phosphate1 (Mg P) 28.42 (± 4.74) 32.54 (± 5.22) 60.96 (± 6.39) 1City of Eureka, 2015

Watershed Runoff

Freshwater runoff nutrient concentration data from the watersheds surrounding

Humboldt Bay are sparse and limited to unpublished reports that differ in location, frequency, time of year, and sampling method. Data from Hurst (2015 b.) only includes

16 samples from one location over the course of two years when salinity was below 5.3 ppt. During the runoff season, the average salinity in Arcata Bay is approximately 30 ppt

(Hurst, 2015 b.; Wiyot Tribe Natural Resources Department, 2015; this study) such that any sample from the surrounding sloughs with salinities of 5.3 ppt would theoretically contain approximately 80% runoff and 20% Bay water. An average of the 16 low salinity samples is used for all mass calculations such that mass discharge is directly proportional to the flow rates applied to each daily discharge calculation. Watershed hydraulic loads were calculated using average daily flow rates from the nearby Little River stream gaging station scaled by the size of individual watersheds.

141

Nutrient concentrations in Freshwater Slough samples collected by Hurst (2015 b.) follow similar seasonal patterns with respect to precipitation and runoff discussed previously for samples collected at Mad River Slough. Data collected at Mad River

Slough contained approximately four years of samples providing better insight into inter- annual variability in watershed runoff, although none of those samples contained sufficiently low salinity to be used to represent freshwater runoff. Data collected at

Freshwater Slough contain only approximately two years of data (n = 55) with an average salinity of 17.3 ppt indicating significant influence by freshwater runoff occurs at this site.

Average annual ammonium and phosphate inputs to Humboldt Bay from watershed runoff are similar (13.8 Mg N/yr and 11.1 Mg P/yr, respectively) while nitrate inputs are approximately five times greater (77.1 Mg N/yr; Table 32). Nitrate in watershed runoff may be from oxidized organic nitrogen and ammonium coming from urban runoff, septic tank leachate, agricultural fertilization, agricultural livestock manure, and naturally occurring organic matter (Castro et al., 2003). Phosphate in freshwater runoff may come from decomposition and re-mineralization of naturally occurring and anthropogenic organic matter, or weathering of geologic formations that may be increased by anthropogenic behaviors such as deforestation (Froelich et al., 1982;

Nedwell et al., 1999). Dissolved silicate is the most abundant dissolved inorganic nutrient supplied by the watershed of Humboldt Bay, although particulate silicon in sediment loads from the watershed may provide a more significant source of silicon to the Bay. Particulate silicon may mineralize once inside the Bay to release dissolved

142 silicate, however particulate silicon contributions from the watershed have not been determined during this study. Silicon is the second most abundant element in the Earth's crust being transported from the land to the sea by weathering of natural geologic formations and watershed runoff (Bianchi, 2013).

Average seasonal watershed runoff to Humboldt Bay may increase by nearly four times during the runoff season, significantly increasing the nutrient loads associated with this source (Table 33 and Table 34). Due to the method of calculating these loads, i.e., using the same flow rate series and a single nutrient concentration value, all percent seasonal changes in loading are equal. Hydraulic and nutrient discharges may increase by nearly 300% during the runoff season in comparison with the low runoff upwelling season.

Table 32 - Annual watershed hydraulic and nutrient loading to Humboldt Bay (and standard deviations).

Humboldt Arcata South Main Constituent Bay Bay Bay Channel 307.3 172.1 33.5 101.6 Discharge1 (Mm3/yr) (± 49.6) (± 27.4) (± 5.5) (± 16.7) 77.1 43.2 8.4 25.5 Nitrate + Nitrite2 (Mg N/yr) (± 62.1) (± 34.8) (± 6.8) (± 20.5) 13.8 7.7 1.5 4.5 Ammonium2 (Mg N/yr) (± 7.8) (± 4.4) (± 0.8) (± 2.6) 11.1 6.2 1.2 3.7 Phosphate2 (Mg P/yr) (± 9.3) (± 5.2) (± 1.0) (± 3.1) 1,093.4 612.4 119.3 361.6 Silicate2 (Mg Si/yr) (± 377.5) (± 211.4) (± 41.2) (± 124.8) 1USGS (2015); 2Hurst (2015 b.)

143

Table 33 - Upwelling season (April-September) watershed hydraulic and nutrient loading to Humboldt Bay (and standard deviations).

Humboldt Arcata South Main Constituent Bay Bay Bay Channel 63.7 35.7 7.0 21.1 Discharge1 (Mm3) (± 36.7) (± 20.3) (± 4.1) (± 12.4) 16.0 9.0 1.7 5.3 Nitrate + Nitrite2 (Mg N) (± 12.9) (± 7.2) (± 1.4) (± 4.3) 2.9 1.6 0.3 0.9 Ammonium2 (Mg N) (± 1.6) (± 0.9) (± 0.2) (± 0.5) 2.3 1.3 0.3 0.8 Phosphate2 (Mg P) (± 1.9) (± 1.1) (± 0.2) (± 0.6) 226.7 127.0 24.7 75.0 Silicate2 (Mg Si) (± 78.3) (± 43.8) (± 8.5) (± 25.9) 1USGS (2015); 2Hurst (2015 b.)

Table 34 - Runoff season (October-March) watershed hydraulic and nutrient loading to Humboldt Bay (and standard deviations)

Humboldt Arcata South Main Constituent Bay Bay Bay Channel 243.6 136.5 26.6 80.6 Discharge1 (Mm3) (± 36.7) (± 20.3) (± 4.1) (± 12.4) 61.1 34.2 6.7 20.2 Nitrate + Nitrite2 (Mg N) (± 12.9) (± 7.2) (± 1.4) (± 4.3) 10.9 6.1 1.2 3.6 Ammonium2 (Mg N) (± 1.6) (± 0.9) (± 0.2) (± 0.5) 8.8 4.9 1.0 2.9 Phosphate2 (Mg P) (± 1.9) (± 1.1) (± 0.2) (± 0.6) 866.7 485.5 94.6 286.7 Silicate2 (Mg Si) (± 78.3) (± 43.8) (± 8.5) (± 25.9) 1USGS (2015); 2Hurst (2015 b.)

Sediment Flux

Intertidal sediments can uptake and release nutrients. Data published by Sin et al.

(2007) indicate that on an annual basis, sediments are a net source of ammonium only,

144 and provide net uptake for nitrate, phosphate, and silicate. For simplicity these data are presented together in a later section for nutrient uptake.

Nutrient Uptake

Major types of dissolved inorganic nutrient uptake in Humboldt Bay have been quantified including phytoplankton production, macroalgae production, eelgrass production, sediment flux, and denitrification. These processes do not necessarily represent permanent sinks as nutrient cycling is a highly dynamic and complex set of processes. Assimilation by phytoplankton, macroalgae, and eelgrass may only act as a temporary storage for nutrients; once the organisms die, their biomass will decay and part of it will re-mineralize, releasing dissolved inorganic nutrients to the water column.

Denitrification is the only sink for DIN included in the mass budgets that results in removal of DIN from the system. Export to the ocean is the only other significant nutrient sink, however this has not been quantified due to complications of determining mixing between nearshore waters and those of the Bay.

Phytoplankton Uptake

Phytoplankton nutrient mass uptake in each bay was calculated using the average monthly volume of each bay (approximately the MSL volume) and average monthly chlorophyll-a concentrations of each bay (Table 35). The Entrance Bay has the largest volume (approximately 32% of the Humboldt Bay volume on average) and experiences the highest average chlorophyll-a concentrations due to the high rate of exchange with nearshore waters (Table 35). Arcata Bay and South Bay experience lower average

145 chlorophyll-a concentrations during the productive upwelling season compared with the other sub-bays due to nutrient limitation, limited exchange with nearshore waters, and zooplankton and shellfish grazing. Arcata Bay contains nearly all of the mariculture shellfish in the Bay so it should be noted that the similarity between South Bay and

Arcata Bay indicates that mariculture has little impact on phytoplankton populations in the Bay.

Table 35 - Average annual and seasonal chlorophyll-a concentrations for sub-bay and average volume of each bay.

Entrance Arcata Main South Constituent Bay Bay Channel Bay Average Volume1 (Mm3) 49 44 36 26 Average Annual 3.3 2.3 3.2 2.3 Chlorophyll-a Concentration (µg/L)2 Average Upwelling Season 5.6 3.5 5.4 3.5 Chlorophyll-a Concentration (µg/L)2 Average Runoff Season 1.3 1.4 1.4 1.0 Chlorophyll-a Concentration (µg/L)2 1Anderson (2015); 2 this study, Harding (1973), Hurst (2009), Hurst (2015 b.), Ryther and Yentsch (1957), Wiyot Tribe Natural Resources Department (2015)

Uncertainty in phytoplankton nutrient uptake is approximately 73% of the mean due to the wide range of uptake rates in the literature used in the calculations. Average annual nitrogen, phosphorus, and silicon uptake by phytoplankton in the Entrance Bay is approximately 51% greater than in Arcata Bay while the volume of the Entrance Bay is only approximately 13% larger (Table 36). This indicates that phytoplankton production in the Entrance Bay is higher than in Arcata Bay per unit volume which may be due to nutrient limitation and phytoplankton grazing in Arcata Bay. Entrance Bay is highly

146 influenced by nearshore waters where phytoplankton production typically begins during the upwelling season. While some of the organic phytoplankton biomass used to calculate nutrient uptake is imported from nearshore waters, phytoplankton reproduction rates of more than two times per day (H.T. Harvey & Associates, 2015) indicate that a significant amount of biomass will be generated inside the Bay due to limited exchange rates that result in residence times of up to 30 days (Anderson, 2010). As phytoplankton populations enter the Bay, chlorophyll-a concentrations decrease moving through each compartment from the Main Channel to Arcata Bay and South Bay due to grazing and nutrient limitation (Table 35). Some of the phytoplankton biomass will re-mineralize and some will either be stored in the biomass of grazers or in sediments as phytoplankton settle out of the water column. The amount of re-mineralization relative to the amount of phytoplankton biomass imported to the system is not clear. However, the high reproduction rates suggest that the net effect of phytoplankton production in the Bay will be a decrease in dissolved inorganic nutrient concentrations in the water column.

Therefore phytoplankton production inside Humboldt Bay is represented as a form of dissolved inorganic nutrient uptake and not a source.

Average upwelling season phytoplankton production increases by over 330% in

Humboldt Bay over runoff season production (Table 37 and Table 38). Seasonal production increases the most in the Main Channel and Entrance Bay (approximately

419% and 383%, respectively) with less seasonal fluctuation in Arcata Bay and South

Bay (244% and 291%, respectively), indicating the Entrance Bay and Main Channel are more productive than Arcata Bay and South Bay during the upwelling season. Higher

147 relative seasonal productivity in the Main Channel than in South Bay may indicate a higher degree of influence from nearshore waters. Further development of a model to estimate phytoplankton nutrient uptake in Humboldt Bay could significantly decrease the range of uncertainty associated with these estimations.

Estimating phytoplankton nutrient uptake and cycling in Humboldt Bay poses one of the largest challenges due to their highly transient nature, high reproduction rate, and soft tissue that readily re-mineralizes to form dissolved inorganic phosphorus and nitrogen for re-uptake. Since phytoplankton production is much higher in nearshore waters (as indicated by higher phytoplankton production rates near the Bay entrance), and decreases significantly inside Humboldt Bay, it can be assumed that phytoplankton import is a significant source of organic matter in the Bay. In the short-term, phytoplankton can uptake significant amounts of inorganic nutrients, though in the long- term they may be a significant source of nutrients.

Humboldt Arcata South Entrance Main Constituent Bay Bay Bay Bay Channel 2,537 607 296 928 707 Nitrogen (Mg N/yr) (± 1,851) (± 443) (± 216) (± 677) (± 516) 351 84 41 128 98 Phosphorus (Mg P/yr) (± 256) (± 61) (± 30) (± 94) (± 71) 5,088 1,216 593 1,860 1,418 Silicon (Mg Si/yr) (± 3,712) (± 887) (± 433) (± 1,357) (± 1,034) *this study, Harding (1973), Hurst (2009), Hurst (2015 b.), Ryther and Yentsch (1957), Wiyot Tribe Natural Resources Department (2015)

148

Table 37 - Upwelling season phytoplankton nutrient uptake for Humboldt Bay and sub- bays (and standard deviations)*.

Humboldt Arcata South Entrance Main Constituent Bay Bay Bay Bay Channel 2,076 490 329 790 467 Nitrogen (Mg N) (± 1,514) (± 358) (± 240) (± 576) (± 341) 287 68 45 109 65 Phosphorus (Mg P) (± 209) (± 49) (± 33) (± 80) (± 47) 4,163 983 659 1,583 937 Silicon (Mg Si) (± 3,037) (± 717) (± 481) (± 1,155) (± 684) *this study, Harding (1973), Hurst (2009), Hurst (2015 b.), Ryther and Yentsch (1957), Wiyot Tribe Natural Resources Department (2015)

Table 38 - Runoff season phytoplankton nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*.

Humboldt Arcata South Entrance Main Constituent Bay Bay Bay Bay Channel 492 150 60 164 118 Nitrogen (Mg N) (± 359) (± 109) (± 44) (± 120) (± 86) 66 21 8 23 16 Phosphorus (Mg P) (± 48) (± 15) (± 6) (± 17) (± 12) 986 300 121 329 237 Silicon (Mg Si) (± 720) (± 219) (± 88) (± 240) (± 173) *this study, Harding (1973), Hurst (2009), Hurst (2015 b.), Ryther and Yentsch (1957), Wiyot Tribe Natural Resources Department (2015)

Macroalgae Uptake

Macroalgae uptake is calculated using monthly carbon uptake proposed by

Pregnall and Rudy (1985), the elemental ratio of carbon, nitrogen, and phosphorus in macroalgae presented by Duarte (1992), and the approximate size of the algal mats estimated by Schlosser and Eicher (2012). The uncertainty reported for calculations of macroalgae production are a product of the standard error reported by Duarte (1992) for the elemental composition of macroalgae by percent of dry weight.

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Arcata Bay and South Bay account for approximately 94% of the total nutrient uptake by macroalgal mats in Humboldt Bay, with the Entrance Bay accounting for only

6% (Table 39). Annual nutrient uptake in Arcata Bay and South Bay differs by only 5% though the surface area of the intertidal mud flats in Arcata Bay is approximately twice that of South Bay, indicating algal mat production may have a significantly larger impact on nutrient uptake in South Bay with respect to the size of the Bay. Pregnall and Rudy

(1985) indicate that macroalgal mats growing in Coos Bay Oregon (approximately 150 miles north of Humboldt Bay) have a growing season between May and November such that production in the runoff season (October-March) accounts for only approximately

8% of the total annual production (Table 40 and Table 41).

Macroalgal mats in Humboldt Bay are washed out of the Bay during late fall storms that introduce high winds and rough waters to the Bay (Schlosser and Eicher,

2012). While a portion of the mats may remain in the Bay being re-mineralized to form dissolved inorganic nutrients, much of the biomass is exported from the system.

However, the amount of macroalgal biomass exported from Humboldt Bay, and the amount that remains a part of the food web inside the Bay is not documented.

Table 39 - Annual macroalgae nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*.

Humboldt Arcata South Entrance Constituent Bay Bay Bay Bay 755 362 343 50 Nitrogen (Mg N/yr) (± 358) (± 160) (± 162) (± 24) 40 19 18 2.7 Phosphorus (Mg P/yr) (± 19) (± 9) (± 9) (± 1.3) *Duarte (1992), Pregnall and Rudy (1985), Schlosser and Eicher (2012)

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Table 40 - Upwelling season macroalgae nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*.

Humboldt Arcata South Entrance Constituent Bay Bay Bay Bay 695 333 316 46 Nitrogen (Mg N) (± 333) (± 160) (± 151) (± 22) 37 18 17 2.4 Phosphorus (Mg P) (± 18) (± 8) (± 8) (± 1.2) *Duarte (1992), Pregnall and Rudy (1985), Schlosser and Eicher (2012)

Table 41 - Runoff season macroalgae nutrient uptake for Humboldt Bay and sub-bays (and standard deviations)*.

Humboldt Arcata South Entrance Constituent Bay Bay Bay Bay 59 29 27 4.0 Nitrogen (Mg N) (± 25) (± 12) (± 11) (± 1.7) 3.1 1.5 1.4 0.2 Phosphorus (Mg P) (± 1.3) (± 0.6) (± 0.6) (± 0.1) *Duarte (1992), Pregnall and Rudy (1985), Schlosser and Eicher (2012)

Eelgrass Uptake

Average monthly eelgrass production was estimated using monthly biomass production measured by Harding (1973), eelgrass bed areal estimates from Schlosser and

Eicher (2012), and the elemental composition of the dominant species of eelgrass in

Humboldt Bay (Zostera marina) reported by Fourqurean et al. (1997). Eelgrass is only seasonally productive with no net production reported during the fall and winter between

August and March (Harding, 1973); therefore all of the annual eelgrass production occurs during the upwelling season. Approximately 63% of all eelgrass production in Humboldt

Bay occurs in Arcata Bay, with 34% occurring in South Bay and only 2% estimated in the Entrance Bay (Table 42). Production in Arcata Bay is approximately 85% higher

151 than in South Bay due to the larger size of the eelgrass beds reported by Schlosser and

Eicher (2012). Note that the small uncertainty reported in eelgrass production is due to use of the standard error in measurements of eelgrass elemental composition (Fourqurean et al., 1997) as this was the only estimate of uncertainty available for this calculation. No information on inter-annual variability of eelgrass bed distribution in Humboldt Bay could be located.

Eelgrass is similar to macroalgae in terms of potential export of nutrients from the

Bay. During the storms of late fall and winter, eelgrass beds are dislodged and significant amounts of eelgrass are flushed out of the Bay on ebbing tides. Some of this biomass may remain in the Bay being re-cycled as part of the benthic food web, though the fraction of total eelgrass production exported and the fraction that remains is not documented.

Humboldt Arcata South Entrance Constituent Bay Bay Bay Bay 301 191 104 6.5 Nitrogen (Mg N/yr) (± 9) (± 6) (± 3) (± 0.2) 49 31 17 1.1 Phosphorus (Mg P/yr) (± 3) (± 2) (± 1) (± 0.1) *Fourqurean et al. (1997), Schlosser and Eicher (2012)

Sediment Flux

Sediment flux may account for uptake and release of various nutrients; however, for simplicity sediment flux data are presented here together. Sediment flux rates

152 measured by Sin et al. (2007) in Lower Yaquina Estuary, Oregon indicate sediments uptake nitrate, phosphate, and silicate, and release ammonium during the upwelling season (Figure 51). These data also indicate that sediments may be a periodic source of phosphate and silicate, and uptake ammonium during the runoff season. Sediment flux may account for a variety of processes such as denitrification, mineralization of organic matter, algal uptake, adsorption, and desorption. For simplicity all of these processes have been grouped into the general process of sediment flux, therefore estimates of sediment flux in Humboldt Bay using values from a different system contain a high degree of uncertainty. Sediment fluxes have been applied to the approximate surface area of the intertidal mud flats between MHHW and MLLW in Humboldt Bay such that the resulting fluxes are directly proportional to the amount of intertidal mud flats in each sub- bay. These estimates do not include fluxes that may occur in sub-tidal sediments and do not account for spatial variation due to differences in sediment type and cover.

On an annual basis, net nitrate flux is into the sediments (uptake) and is nearly three times greater than ammonium flux from the sediments (release) indicating

Humboldt Bay's intertidal mud flats may provide significant storage for dissolved inorganic nitrogen (Table 43). During the upwelling season, nitrate uptake is nearly twice as great as ammonium release, resulting in significant sediment DIN uptake.

However, during the runoff season, higher net DIN uptake occurs due to ammonium uptake. It should be noted that during the study conducted by Sin et al. (2007), used to estimate sediment fluxes in Humboldt Bay, nitrate concentrations in the water column increased during this period due to ocean upwelling, whereas nitrate concentrations in

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Arcata Bay decrease during the upwelling season due to high productivity and limited tidal exchange. Sediment nitrate uptake has been found to be proportional to water column nitrate concentrations such that lower nitrate concentrations may result in lower sediment flux rates (Boynton and Kemp, 1985). Therefore, estimates of sediment nitrate uptake from Sin et al. (2007) may represent a high estimate.

Seasonal sediment ammonium fluxes change by approximately 460%, from uptake (negative flux) during the runoff season, to release (positive flux) during the upwelling season. Ammonium released from sediments may indicate that higher temperatures during the upwelling season result in increased re-mineralization of ammonium from decomposing organic matter. During this time, algal production is at a maximum such that any increase in ammonium efflux from sediments would be in excess of metabolic demand by benthic organisms.

Phosphate uptake by sediments may increase by approximately 330% during the upwelling season (Table 44 and Table 45), due to either uptake by benthic algae or increased chemical adsorption to ferric oxyhydrides that occurs in the presence of oxygen

(Conley et al., 1995). Average dissolved oxygen concentrations in the water column of

Humboldt Bay are higher during the runoff season. However, photosynthesizing algae on the intertidal mud flats during the upwelling season produce oxygen that may increase adsorption of phosphate. The difference between benthic dissolved oxygen and water column dissolved oxygen has not been documented in Humboldt Bay therefore the potential for phosphate adsorption has not been determined.

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Silicate sediment flux changes from release (positive flux) during the runoff season to uptake (negative flux) during the upwelling season (Figure 51). Silicate release from sediments during the runoff season may be an indicator of mineralization of particulate matter from watershed sediment loads or re-mineralization of diatomaceous material accumulated during the upwelling season. Sediment loads from watershed runoff may be a significant source of particulate silicon to the system that have not been accounted for during this study. High silicate uptake during the upwelling season may be due to benthic diatom production, although this form of uptake has also not been determined in Humboldt Bay. Silicate release during the runoff season occurred during

December and January according to data gathered by Sin et al. (2007). The magnitude of the release was equal to approximately 87% of the total uptake during the rest of the year, and occurred following precipitation events between September and December. This indicates that significant silicate release from sediments may be due to recently deposited siliceous material from watershed runoff.

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Figure 51 - Average monthly intertidal sediment nutrient fluxes using flux rates from Sin et al. (2007) and the intertidal surface area of Humboldt Bay.

Table 43 - Annual sediment nutrient flux for Humboldt Bay and sub-bays (and standard deviations)*; negative flux values indicate uptake by sediments.

Humboldt Arcata South Entrance Main Constituent Bay Bay Bay Bay Channel -129 -83 -40 -1.4 -3.9 Nitrate (Mg N/yr) (± 52) (± 33) (± 16) (± 0.6) (± 1.6) 33 21 10 0.4 1 Ammonium (Mg N/yr) (± 214) (± 138) (± 67) (± 2.4) (± 6) -13 -8 -4 -0.1 -0.4 Phosphate (Mg P/yr) (± 37) (± 24) (± 12) (± 0.4) (± 1.1) -34 -22 -11 -0.4 -1 Silicate (Mg Si/yr) (± 38) (± 24) (± 12) (± 0.4) (± 1) *Anderson (2015), Sin et al. (2007)

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Table 44 - Upwelling season sediment nutrient flux for Humboldt Bay and sub-bays (and standard deviations)*; negative flux values indicate uptake by sediments.

Humboldt Arcata South Entrance Main Constituent Bay Bay Bay Bay Channel -89 -58 -28 -1 -3 Nitrate (Mg N) (± 66) (± 42) (± 20) (± 1) (± 2) 46 30 14 0.5 1 Ammonium (Mg N) (± 559) (± 361) (± 175) (± 6.1) (± 17) -10 -6.6 -3 -0.1 -0.3 Phosphate (Mg P) (± 46) (± 30) (± 15) (± 0.5) (± 1.4) -208 -134 -65 -2.3 -6 Silicate (Mg Si) (± 171) (± 111) (± 54) (± 1.9) (± 5) *Anderson (2015), Sin et al. (2007)

Table 45 - Runoff season sediment nutrient flux for Humboldt Bay and sub-bays (and standard deviations)*; negative flux values indicate uptake by sediments.

Humboldt Arcata South Entrance Main Constituent Bay Bay Bay Bay Channel -40 -26 -13 -0.4 -1.2 Nitrate (Mg N) (± 3) (± 2) (± 1) (± 0.03) (± 0.1) -15 -8 -4 -0.1 -0.4 Ammonium (Mg N) (± 10) (± 6) (± 3) (± 0.1) (± 0.3) -2 -2 -1 -0.03 -0.1 Phosphate (Mg P) (± 3) (± 2) (± 1) (± 0.03) (± 0.1) 174 112 54 2 5 Silicate (Mg Si) (± 246) (± 159) (± 77) (± 3) (± 7) *Anderson (2015), Sin et al. (2007)

Denitrification

Annual denitrification in Humboldt Bay may account for approximately 768 Mg

N removal from the system (Table 46). No data were provided by Dollar et al. (1991) for seasonal variation in denitrification determined for Tomales Bay, so upwelling and runoff season denitrification are equal to one-half the annual estimate. Since the same areal denitrification rate was applied to each sub-bay of Humboldt Bay, the relative

157 magnitudes of denitrification are proportional to the relative surface area of each bay.

Denitrification is assumed to be a benthic process that occurs due to various species of bacteria in the sediments, thus denitrification rates are relative to the surface area of each bay and not volume. Given the relative size of each sub-bay, Arcata Bay makes up approximately 54% of the total estimated denitrification in Humboldt Bay, and South

Bay, Entrance Bay, and the Main Channel make up approximately 26%, 12%, and 9% respectively.

The bacterial cycle of denitrification involves multiple steps and species of bacteria, each of which is governed by different factors such as labile carbon availability, alkalinity, temperature, and inorganic nitrogen availability. The method used here to estimate denitrification in Humboldt Bay simplifies all of these processes into a single empirical rate estimate from a similar system that does not account for any of these factors.

Table 46 - Annual denitrification in Humboldt Bay and sub-bays (and standard deviations).

Humboldt Arcata South Entrance Main Constituent Bay Bay Bay Bay Channel 768 414 198 90 66 DIN* (Mg N/yr) (± 462) (± 249) (± 119) (± 54) (± 40) *Anderson (2015), Dollar et al. (1991), Smith et al. (1991)

Water Budget

Average annual inflows to Humboldt Bay (Table 47) indicate that total tidal inflow is over two orders of magnitude greater than all other inflows combined, with

158 wastewater being the smallest contributor. Tidal exchange volume for the whole Bay, approximately 14% of the total tidal inflow for Humboldt Bay, is over one order of magnitude greater than all other sources combined. The tidal exchange volume is a product of the total tidal influx and the individual exchange rates for each sub-bay. This indicates that even with limited tidal exchange, the ocean end member is still the most substantial hydraulic input to Humboldt Bay.

Watershed flows contain were calculated using flow rates from nearby Little

River scaled by the size of each individual watershed and do not represent actual streamflows from each source to the Bay. Watershed inflows estimated for Humboldt

Bay are equal to approximately 4% of the tidal exchange volumes, and are over 34 times greater than wastewater inflows (Table 47).

Average annual wastewater inflows to Humboldt Bay are the smallest hydraulic input compared with tidal exchange, watershed runoff, and precipitation (Table 47).

Wastewater is equal to approximately 0.1% of the estimated tidal exchange volumes, 3% of watershed runoff, and 13% of precipitation falling directly on the Bay annually. In

Arcata Bay, the AWTF discharge is equal to approximately 0.4% of the estimated annual tidal exchange volume, 1.5% of watershed runoff volumes, and 6.9% of direct precipitation falling on Arcata Bay.

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Humboldt Arcata South Entrance Main Water Source Bay Bay Bay Bay Channel Total Tidal Inflow1 66,874 35,653 17,272 67,558 42,293 Tidal Flushing2 8,299 594 617 21,112 6,131 Watershed Runoff3 307 172 34 NA* 102 Direct Precipitation4 69.3 37.4 17.9 8.1 5.9 WWTF5 8.88 2.58 NA NA 6.30 1Anderson (2015); 2Anderson (2010) and Anderson (2015); 3USGS (2015) and WBD (2015); 4WRCC (2015); 5City of Arcata (2015) and City of Eureka (2015)

Wastewater hydraulic loads increase by approximately 280% during the runoff season due to infiltration in collection systems and direct precipitation on oxidation ponds and constructed wetlands. Watershed runoff increases by nearly 300% during the runoff season due to precipitation on the watershed, and precipitation directly falling on the Bay increases by nearly 400% during the runoff season (Table 48 and Table 49). Lower watershed runoff with respect to precipitation may be due to water that becomes entrained in sediments and groundwater, terrestrial evaporation, or due to the indirect method of using Little River flow data to calculate stream flows for Humboldt Bay.

Precipitation data, on the other hand, are from a weather station inside Humboldt Bay.

Discharge from the AWTF increases by approximately 65% during the runoff season due to the large open water surface area of the pond and wetland treatment system

(approximately 90 acres, or 0.36 Mm2), and inflow and infiltration into the municipal wastewater collection system. Discharge from the EWTF only increases by

160 approximately 15%, due to inflow and infiltration into their municipal wastewater collection system. Tidal volumes change little between seasons due to the large magnitude of the flow rates. Small seasonal variation in tidal flux is the result of varying tidal elevations between seasons, and other environmental factors that may be included in the hydrodynamic model from which they were derived.

Table 48 - Upwelling season water budget for Humboldt Bay (Mm3).

Humboldt Arcata South Entrance Main Water Source Bay Bay Bay Bay Channel Total Tidal Inflow1 33,543 17,756 8,580 33,631 21,062 Tidal Flushing2 4,163 296 306 10,510 3,053 Watershed Runoff3 63.7 35.7 7.0 NA 21.1 Direct Precipitation4 11.7 6.3 3.0 1.4 1.0 WWTF5 3.91 0.98 NA NA 2.94 1Anderson (2015); 2Anderson (2010) and Anderson (2015); 3USGS (2015) and WBD (2015); 4WRCC (2015); 5City of Arcata (2015) and City of Eureka (2015)

Table 49 - Runoff season water budget for Humboldt Bay (Mm3).

Humboldt Arcata South Entrance Main Water Source Bay Bay Bay Bay Channel Total Tidal Inflow1 33,331 17,897 8,692 33,927 21,232 Tidal Flushing2 4,136 298 310 10,602 3,078 Watershed Runoff3 244 136 27 NA 81 Direct Precipitation4 57.7 31.1 14.9 6.7 4.9 WWTF5 4.97 1.61 NA NA 3.36 1Anderson (2015); 2Anderson (2010) and Anderson (2015); 3USGS (2015) and WBD (2015); 4WRCC (2015); 5City of Arcata (2015) and City of Eureka (2015)

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Nutrient Budgets

Annual and seasonal dissolved inorganic nitrogen, phosphorus, and silicon budgets are included in the following sections containing sources and uptake estimations for Humboldt Bay as a whole, and each sub-bay individually. Dissolved inorganic nutrient loading to Arcata Bay, South Bay, and the Main Channel from the ocean were calculated using flushing rate estimations from Anderson (2010). Dissolved inorganic nutrients entering the Bay from the ocean are entrained in the Entrance Bay and the Main

Channel before entering Arcata Bay, allowing time for biological processes to influence actual influent nutrient loads. These processes are complex and vary with time and space making an accurate estimation of uptake and release in each compartment difficult and beyond the scope of this project. Dissolved inorganic nutrients may be taken up as they enter the Bay and then re-cycled as the plant material lyses nutrients upon expiration.

Therefore dissolved inorganic nutrients that are consumed and incorporated into organic material may be re-introduced to another part of the Bay as dissolved inorganic nutrients multiple times during the residence time of the Bay.

Annual DIN Budget

DIN uptake estimates for phytoplankton, macroalgae, and eelgrass do not include individual speciation for nitrate, nitrite, and ammonium because these estimates were calculated using elemental biomass content of nitrogen. Therefore, budgets are presented with respect to DIN only. Standard deviations reported for types of uptake

(phytoplankton uptake, macroalgae uptake, eelgrass uptake, sediment flux, and

162 denitrification) are products of standard deviations reported by the literature sources used to calculate these forms of uptake and do not represent inter-annual variability. Standard deviations reported for wastewater loading are the product of multiple years of sampling, and do represent inter-annual variability in these sources. Uncertainty in watershed loading represents inter-annual variability in flows from Little River stream gage station as a single average nutrient concentration was used in all calculations of watershed discharge. It should be noted that inter-annual standard deviations were calculated for phytoplankton uptake based on variations in average chlorophyll-a concentrations, although the larger and more conservative estimate of uncertainty from the wide range of uptake rates in the literature was used instead.

Average annual DIN loading to Humboldt Bay is dominated by ocean exchange with watershed runoff and wastewater contributing only 0.6% and 1.0%, respectively

(Table 50). Average annual DIN uptake accounts for only 31% of sources, indicating a significant sink is unaccounted for in this budget. Advective transport of DIN out of the

Bay with the ebbing tides may account for this as the exchange rates in the Entrance Bay and Main Channel (0.31 and 0.14 respectively) are much higher than for Arcata Bay and

South Bay (0.02 and 0.04 respectively) as indicated by Anderson (2010). To illustrate this point, multiplying the low tide Bay entrance sample DIN concentrations by the ebb tide volume at the time of the sample indicates annual export could account for over

16,000 Mg N/yr (Table 51) which is greater than the estimated average annual DIN import from the ocean (14,363 Mg N/yr). The difference in estimations of import and export are due to the differences between datasets used for each calculation; only one

163 year of low tide data are available at the Bay entrance whereas there are multiple years of data for high tide samples. This example is only to illustrate that the potential magnitude of advective export from the Bay may be on a similar scale as advective import. This suggests that export of dissolved nutrients through tidal exchange may be the largest pathway for nutrient removal from Humboldt Bay. Advective export of dissolved inorganic nutrients from Humboldt Bay also includes internal mineralization from organic matter such that export of dissolved inorganic nutrients may be greater than import.

Phytoplankton uptake is the largest potential type of DIN uptake in Humboldt Bay

(Table 50) accounting for approximately 57% of all DIN uptake. This is followed by macroalgae (17%), denitrification (17%), eelgrass (7%), and sediment flux (2%).

Wastewater DIN loading (149 Mg N/yr) is less than estimates of uptake, with the exception of sediment flux (96 Mg N/yr). This indicates that wastewater DIN discharge to Humboldt Bay is minor in comparison with estimations of uptake and may play a minor role in stimulating biological production in the Bay annually.

Arcata Bay and South Bay indicate net-negative average annual DIN balances may exist, suggesting high productivity relative to DIN inputs (Table 50). Comparing total annual DIN uptake in South Bay and Arcata Bay based upon MSL volume of each indicates a similar rate of DIN uptake occurs in each bay (Table 52). DIN loading is significantly higher in South Bay due to the proximity to the ocean and higher tidal flushing rate (Table 52). The AWTF and watershed runoff make up approximately 12% and 15% of the annual DIN load to Arcata Bay, respectively, indicating freshwater

164 sources of DIN are minor contributors to DIN-stimulated production in Arcata Bay. The combined average annual wastewater DIN load to Humboldt Bay is approximately 64% larger than the total watershed DIN load due to potential discharges from the EWTF.

Whereas in Arcata Bay, the AWTF DIN load is only approximately 78% of the watershed load on average. Note that 86% of the estimated EWTF DIN load is made up of nitrate which is based upon a single effluent nitrate measurement and may not represent the true average effluent concentration resulting in significant over or under- estimation.

In South Bay, watershed runoff makes up approximately 2% of the average annual DIN load with the ocean accounting for the other 98% (Table 50). Average annual DIN uptake in South Bay includes macroalgae (35%), phytoplankton (30%), denitrification (20%), and eelgrass production (11%) with sediment flux accounting for only approximately 3% of the total uptake. In Arcata Bay, DIN uptake consists of phytoplankton uptake (37%), denitrification (25%), macroalgae uptake (22%), eelgrass uptake (12%), and sediment flux (4%). Denitrification and eelgrass production in Arcata

Bay are 109% and 84% greater than in South Bay, respectively, due to the relative size of each.

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Table 50 - Annual DIN budget including loading and uptake for Humboldt Bay and sub- bays (Mg N/yr); negative values denote uptake or removal from the system.

Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 14,363 239 513 4,488 2,082 Ocean1,2,3 (± 705) (± 12) (± 25) (± 220) (± 102) 149 40 109 WWTF4 NA NA (± 25) (± 15) (± 14) 91 51 10 30 Watershed3,5 NA (± 70) (± 39) (± 8) (± 23) -2,537 -607 -296 -928 -707 Phytoplankton2,3,5,6 (± 1,851) (± 443) (± 216) (± 677) (± 516) -755 -362 -343 -50 Macroalgae7,8 NA (± 358) (± 171) (± 162) (± 24) -768 -414 -198 -90 -66 Denitrification1,9 (± 462) (± 249) (± 119) (± 54) (± 40) -301 -191 -104 -7 Eelgrass8,10 NA (± 6) (± 6) (± 3) (± 0.2) -96 -62 -30 -1 -2.9 Sediment Flux1,11 (± 233) (± 151) (± 73) (± 3) (± 7) 10,146 -1,305 -447 3,413 1,445 Net (± 3,710) (± 1,086) (± 606) (± 978) (± 702) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4City of Arcata (2015) and City of Eureka (2015); 5Hurst (2009) and Hurst (2015 b.); 6Harding (1973) and Ryther and Yentsch (1957); 7Duarte (1992), Pregnall and Rudy (1985); 8Schlosser and Eicher (2012); 9Dollar et al. (1991) and Smith et al. (1991); 10Fourqurean et al. (1997); 11Sin et al. (2007)

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DIN Ebb Flow* Export Export Date (µM) (Mm3/tide) (Mg N/tide) (Mg N/mo) 1/20/2014 14.5 79 16 995 3/22/2014 22.5 110 35 2,162 6/3/2014 15.1 93 20 1,173 6/16/2014 17.6 139 34 2,053 7/17/2014 17.7 107 26 1,641 8/13/2014 8.0 130 15 906 9/12/2014 19.2 106 28 1,706 10/12/2014 9.6 70 9 586 11/2/2014 20.3 101 29 1,718 12/30/2014 9.0 117 15 913 2/1/2015 9.6 124 17 1,034 2/10/2015 22.0 87 27 1,662 *Anderson (2015)

Table 52 - Annual volumetric DIN loading and uptake rates for Humboldt Bay and sub- bays.

Humboldt Arcata South Entrance Main Loading/Uptake Rate Bay Bay Bay Bay Channel Loading Rate1,2 (g N/m3/yr) 150 9 21 91 62 Uptake Rate1,3 (g N/m3/yr) -60 -42 -40 -22 -22 1Anderson (2015), Hurst (2009), Hurst (2015 b.), this study, Wiyot Tribe Natural Resources Department (2015); 2City of Arcata (2015), City of Eureka (2015); 3Dollar et al. (1991), Duarte (1992), Fourqurean et al. (1997), Harding (1973), Pregnall and Rudy (1985), Ryther and Yentsch (1957), Schlosser and Eicher (2012), Sin et al. (2007), Smith et al. (1991),

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Seasonal DIN Budgets

Average DIN loading to Humboldt Bay is dominated by nearshore influences during the runoff and upwelling seasons making up approximately 98% and 99% of the loads respectively (Table 54 and Table 55). Although ocean upwelling significantly increases DIN loading to the Bay during the upwelling season compared with the runoff season (20% increase), this source far outweighs all other inputs combined throughout the year. Total DIN uptake in Humboldt Bay increases by approximately 250% during the upwelling season due to phytoplankton production (increases by over 300%), macroalgae production (nearly all macroalgae production occurs during the upwelling season), and eelgrass production (100% of the annual eelgrass production is assumed to occur during the upwelling season). Sediment DIN uptake decreases during the upwelling season by nearly 20% compared with the runoff season due to algal and bacterial assimilation of nutrients mineralized in sediments.

Wastewater and watershed DIN loading decrease by 28 Mg N and 53 Mg N, 68% and 26%, respectively, during the upwelling season indicating that these sources have a natural pattern of reducing DIN output during the productive season in Humboldt Bay.

The majority of the decrease in DIN loading to the Bay from wastewater sources during the upwelling season is due to the AWTF, the AWTF DIN load decreases by 24 Mg N while the EWTF load decreases by 4 Mg N. The natural relationship between patterns of increased productivity in Humboldt Bay and decreased DIN discharge from the AWTF reduces the potential impact of the AWTF discharge on stimulating production in the

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Bay. However, there is no indication that DIN discharges from either WWTF are significant enough to contribute to over-production in the Bay.

Table 53 - Upwelling season DIN loading and uptake for Humboldt Bay and sub-bays (Mg N).

Humboldt South Entrance Main Source/Uptake Bay Arcata Bay Bay Bay Channel 7,832 131 280 2,448 1,135 Ocean1,2,3 (± 705) (± 12) (± 25) (± 220) (± 102) 60 8 53 WWTF4 (± 21) (± 5) NA NA (± 11) 19 11 2 6 Watershed3,5 (± 14) (± 8) (± 2) NA (± 5) -2,045 -457 -235 -764 -589 Phytoplankton2,3,5,6 (± 1,492) (± 333) (± 172) (± 557) (± 430) -695 -333 -316 -46 Macroalgae7,8 (± 333) (± 160) (± 151) (± 22) NA -384 -207 -99 -45 -33 Denitrification1,9 (± 231) (± 125) (± 60) (± 27) (± 20) -301 -191 -104 -7 Eelgrass8,10 (± 9) (± 6) (± 3) (± 0.2) NA -43 -28 -13 -1 -1 Sediment Flux1,11 (± 624) (± 403) (± 195) (± 7) (± 19) 4,443 -1,067 -486 1,585 571 Net (± 3,430) (± 1,051) (± 608) (± 834) (± 586) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4City of Arcata (2015) and City of Eureka (2015); 5Hurst (2009) and Hurst (2015 b.); 6Harding (1973) and Ryther and Yentsch (1957); 7Duarte (1992), Pregnall and Rudy (1985); 8Schlosser and Eicher (2012); 9Dollar et al. (1991) and Smith et al. (1991); 10Fourqurean et al. (1997); 11Sin et al. (2007)

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Table 54 - Runoff season DIN loading and uptake for Humboldt Bay and sub-bays (Mg N).

Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 6,531 109 233 2,041 947 Ocean1,2,3 (± 1,225) (± 20) (± 44) (± 383) (± 178) 88 32 56 WWTF4 NA NA (± 9) (± 9) (± 12) 72 40 8 24 Watershed3,5 NA (± 55) (± 8) (± 6) (± 18) -492 -150 -60 -164 -118 Phytoplankton2,3,5,6 (± 359) (± 109) (± 44) (± 120) (± 86) -59 -29 -27 -4 Macroalgae7,8 NA (± 25) (± 12) (± 11) (± 2) -384 -207 -99 -45 -33 Denitrification1,9 (± 231) (± 125) (± 60) (± 27) (± 20) Eelgrass8,10 0.0 0.0 0.0 0.0 NA -53 -34 -17 -1 -2 Sediment Flux1,11 (± 12) (± 8) (± 4) (± 0.1) (± 0.4) 5,703 -238 38 1,827 874 Net (± 1,917) (± 291) (± 169) (± 531) (± 314) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4City of Arcata (2015) and City of Eureka (2015); 5Hurst (2009) and Hurst (2015 b.); 6Harding (1973) and Ryther and Yentsch (1957); 7Duarte (1992), Pregnall and Rudy (1985); 8Schlosser and Eicher (2012); 9Dollar et al. (1991) and Smith et al. (1991); 10Fourqurean et al. (1997); 11Sin et al. (2007)

Annual Phosphate-P Budget

Annual phosphate-P loading and removal is dominated by ocean loading and phytoplankton uptake (97% and 78%, respectively). Wastewater accounts for approximately 3% of the total phosphate-P load to Humboldt Bay and the AWTF contributes approximately 21% of the total load to Arcata Bay (Table 55). Annual wastewater phosphate-P loads to Humboldt Bay are equal to 16% of the total uptake, with phytoplankton uptake being nearly 375% greater than wastewater loads. Combined

170 wastewater and watershed loading of phosphate-P is equal to approximately 44% of the tidal influx from nearshore waters. This indicates that freshwater phosphate-P loads to

Arcata Bay may have significant impacts on phosphate concentrations in the Bay. As mentioned previously, phosphate is not a limiting nutrient in Humboldt Bay such that an excess of phosphate in the Bay is not expected to stimulate biological production. The

EWTF phosphate-P discharge may be over four times as great as AWTF annually, though only one measurement of phosphate-P from the EWTF was available. The annual net balance in phosphate-P loading and uptake in Humboldt Bay is net-positive, whereby uptake only accounts for approximately 17% of loading to the Bay. This indicates a significant amount of phosphate-P may be returned to the ocean through advection of ebbing tides.

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Table 55 - Annual phosphate-P loading and uptake for Humboldt Bay and sub-bays (Mg P/yr).

Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 2,653 44 95 829 385 Ocean1,2,3 (± 191) (± 3) (± 7) (± 60) (± 28) 74 13 61 WWTF4 NA NA (± 4) (± 2) (± 6) 11 6 1 4 Watershed3,5 NA (± 2) (± 1) (± 0.2) (± 1) -351 -84 -41 -128 -98 Phytoplankton2,3,5,6 (± 256) (± 61) (± 30) (± 94) (± 71) -40 -19 -18 -18 Macroalgae7,8 NA (± 19) (± 9) (± 9) (± 1) -49 -31 -17 -1 Eelgrass8,9 NA (± 3) (± 2) (± 1) (± 0.1) 13 -8 -4 -0.1 17 Sediment Flux1,10 (± 25) (± 16) (± 8) (± 0.3) (± 1) 2,286 -79 16 682 351 Net (± 499) (± 94) (± 54) (± 155) (± 107) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4City of Arcata (2015) and City of Eureka (2015); 5Hurst (2009) and Hurst (2015 b.); 6Harding (1973) and Ryther and Yentsch (1957); 7Duarte (1992), Pregnall and Rudy (1985); 8Schlosser and Eicher (2012); 9Fourqurean et al. (1997); 10Sin et al. (2007)

Seasonal Phosphate-P Budgets

Seasonal phosphate-P loading to Humboldt Bay is dominated by nearshore influences during upwelling and runoff seasons contributing approximately 98% and 96% of the total phosphate-P loads, respectively. Total phosphate-P loading to Humboldt Bay increases by approximately 12% during the upwelling season due to ocean upwelling whereas wastewater and watershed phosphate-P contributions decrease by 20% and 74%, respectively. AWTF phosphate-P loading nearly doubles during the runoff season compared to the upwelling season as vegetation in the natural treatment system senesces,

172 releasing phosphate-P into the water column and flow rates increase due to rainfall. The net seasonal phosphate-P balance between loading and uptake in Humboldt Bay remains positive during both seasons indicating an excess of phosphate-P is available to the system. The net phosphate-P balances in Arcata Bay and South Bay are net-negative during the upwelling season, indicating a high level of uptake with respect to loading.

During the upwelling season, phosphate-P uptake in Arcata Bay and South Bay is approximately 300% and 40% greater than loading, respectively. Since phosphate-P is not a limiting nutrient in Arcata Bay, the net deficit during the upwelling season in Arcata

Bay and South Bay indicates estimations of phosphate-P uptake may be high or phosphate-P loading may be low.

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Table 56 - Upwelling season phosphate-P loading and uptake for Humboldt Bay and sub- bays (Mg P).

Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 1,404 23 50 439 203 Ocean1,2,3 (± 440) (± 7) (± 16) (± 137) (± 64) 33 5 28 WWTF4 NA NA (± 4) (± 0.5) (± 5) 2 1 0.3 1 Watershed3,5 NA (± 1) (± 1) (± 0.1) (± 0.4) -283 -63 -33 -106 -81 Phytoplankton2,3,5,6 (± 206) (± 46) (± 24) (± 77) (± 59) -37 -18 -17 -17 Macroalgae7,8 0 (± 18) (± 8) (± 8) (± 1) -49 -31 -17 -1 Eelgrass8,9 0 (± 3) (± 2) (± 1) (± 0.1) -10 -7 -3 -0.1 -0.3 Sediment Flux1,10 (± 46) (± 30) (± 15) (± 0.5) (± 1) 1,061 -89 -19 315 151 Net (± 718) (± 95) (± 63) (± 216) (± 130) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4City of Arcata (2015) and City of Eureka (2015); 5Hurst (2009) and Hurst (2015 b.); 6Harding (1973) and Ryther and Yentsch (1957); 7Duarte (1992), Pregnall and Rudy (1985); 8Schlosser and Eicher (2012); 9Fourqurean et al. (1997); 10Sin et al. (2007)

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Table 57 - Runoff season phosphate-P loading and uptake for Humboldt Bay and sub- bays (Mg P).

Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 1,250 21 45 390 181 Ocean1,2,3 (± 249) (± 4) (± 9) (± 78) (± 36) 41 9 33 WWTF4 NA NA (± 7) (± 2) (± 5) 9 5 1 3 Watershed3,5 NA (± 2) (± 1) (± 0.2) (± 1) -68 -21 -8 -23 -16 Phytoplankton2,3,5,6 (± 50) (± 15) (± 6) (± 17) (± 12) -3 -2 -1 -1 Macroalgae7,8 0 (± 1) (± 1) (± 1) (± 0.1) Eelgrass8,9 0 0 0 0 0 -2 -2 -1 -0.03 -0.1 Sediment Flux1,10 (± 3) (± 2) (± 1) (± 0.03) (± 0.1) 1,226 11 35 366 200 Net (± 312) (± 25) (± 17) (± 94) (± 54) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4City of Arcata (2015) and City of Eureka (2015); 5Hurst (2009) and Hurst (2015 b.); 6Harding (1973) and Ryther and Yentsch (1957); 7Duarte (1992), Pregnall and Rudy (1985); 8Schlosser and Eicher (2012); 9Fourqurean et al. (1997); 10Sin et al. (2007)

Annual Silicate-Si Budget

Tidal influx is the major source of silicate-Si to Humboldt Bay comprising 97% of the total annual inputs, with the remaining 3% of the load coming from the watershed

(Table 58). The silicate-Si content of wastewater has not been determined, although it is unlikely that it is significantly greater than watershed runoff as silicate is typically derived from weathering of geologic formations. Phytoplankton uptake calculations assume 100% of the phytoplankton populations are diatoms which may not be the case, making this an upper estimate of possible phytoplankton silicate-Si uptake. Watershed

175 silicate-Si loading in Arcata Bay contributes approximately 53% of the total input annually indicating that watershed runoff is a significant source of silicate-Si in Arcata

Bay. The net-negative annual silicate balance in Arcata Bay indicates that estimations of uptake are high as silicate is not a limiting nutrient in the Bay. This is likely due to the high estimation of phytoplankton uptake based upon the assumption that all phytoplankton are diatoms.

Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 32,998 550 1,179 10,312 4,784 Ocean1,2,3 (± 3,188) (± 53) (± 114) (± 996) (± 462) 1,093 612 119 362 Watershed3,4 NA (± 177) (± 98) (± 20) (± 59) -5,088 -1,216 -593 -1,860 -1,418 Phytoplankton2,3,4,5 (± 3,712) (± 887) (± 433) (± 1,357) (± 1,034) -34 -22 -11 -0.4 -1 Sediment Flux1,6 (± 50) (± 33) (± 16) (± 1) (± 2) 28,970 -76 694 8,451 3,726 Net (± 7,126) (± 1,071) (± 582) (± 2,354) (± 1,557) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4Hurst (2009) and Hurst (2015 b.); 5Harding (1973) and Ryther and Yentsch (1957); 6Sin et al. (2007)

Seasonal Silicate-Si Budgets

Seasonal silicate-Si loading to Humboldt Bay is dominated by nearshore influences during the runoff and upwelling seasons contributing 94% and 99% of the total loads respectively (Table 59 and Table 60). Phytoplankton silicate-Si uptake may be approximately 200-400% higher during the upwelling season in the various sub-bays

176 of Humboldt Bay. Sediment silicate-Si flux changes from uptake (negative flux) to release (positive flux) between the upwelling and runoff seasons. This indicates benthic diatoms may be a significant form of uptake for silicate-Si during the upwelling season and mineralization may be a significant source during the runoff season. Estimated sediment release of silicate-Si during the runoff season may equal 33% and 81% of the watershed load in Arcata Bay and South Bay respectively. Watershed silicate-Si loading to Humboldt Bay increases by approximately 280% during the runoff season due to increased runoff.

Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 16,860 281 602 5,269 2,444 Ocean1,2,3 (± 3,964) (± 66) (± 142) (± 1,239) (± 575) 227 127 25 75 Watershed3,4 NA (± 131) (± 72) (± 15) (± 44) -4,101 -916 -472 -1,532 -1,181 Phytoplankton2,3,4,5 (± 2,992) (± 668) (± 344) (± 1,117) (± 862) -208 -134 -65 -2 -6 Sediment Flux1,6 (± 171) (± 111) (± 54) (± 2) (± 5) 12,777 -643 90 3,735 1,332 Net (± 7,257) (± 917) (± 554) (± 2,358) (± 1,485) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4Hurst (2009) and Hurst (2015 b.); 5Harding (1973) and Ryther and Yentsch (1957); 6Sin et al. (2007)

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Humboldt Arcata South Entrance Main Source/Uptake Bay Bay Bay Bay Channel 16,138 269 576 5,043 2,339 Ocean1,2,3 (± 776) (± 13) (± 28) (± 242) (± 112) 867 485 95 287 Watershed3,4 NA (± 166) (± 92) (± 18) (± 56) -986 -300 -121 -329 -237 Phytoplankton2,3,4,5 (± 720) (± 219) (± 88) (± 240) (± 173) 174 112 54 2 5 Sediment Flux1,6 (± 246) (± 159) (± 77) (± 3) (± 7) 16,193 567 605 4,716 2,395 Net (± 1,907) (± 482) (± 211) (± 485) (± 348) 1Anderson (2015); 2This study; 3Wiyot Tribe Natural Resources Department (2015); 4Hurst (2009) and Hurst (2015 b.); 5Harding (1973) and Ryther and Yentsch (1957); 6Sin et al. (2007)

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DISCUSSION

Seasonal Responses

Ocean upwelling increases DIN, phosphate-P, and silicate-Si loads to Humboldt

Bay by approximately 20%, 12%, and 4%, respectively, while uptake increases by approximately 248%, 406%, and 418%, respectively, indicating other environmental factors such as sunlight and temperature play significant roles in increased biological production. During the productive upwelling season, combined wastewater and watershed DIN and phosphate-P loads decrease by approximately 50% and 30%, respectively, indicating dissolved inorganic nutrient loading from freshwater sources is naturally offset from patterns of biological productivity in Humboldt Bay. The AWTF

DIN load decreases by approximately 75% (24 Mg N) on average during the upwelling season compared to the runoff season. The upwelling season AWTF DIN load (8 Mg N) is also minor with respect to increases in uptake by phytoplankton (307 Mg N), macroalgae (305 Mg N), eelgrass (191 Mg N), and sediments (28 Mg N).

Phosphate-P concentrations increase throughout the Bay during the upwelling season as ocean upwelling increases the load from the ocean to the Bay and internal sources increase supply. Concentrations of phosphate-P in Arcata Bay are higher than at the Bay entrance due to either freshwater sources, re-mineralization of organic matter, or desorption from sediments. While freshwater phosphate-P loads are lower during the upwelling season, the AWTF discharge contributes approximately 16% of the total load to Arcata Bay. Applying the average upwelling season phosphate-P discharge from the

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AWTF (0.025 Mg P/d) to the MSL volume of Arcata Bay (38.5 Mm3) results in a potential increase in concentration of the whole Bay of approximately 0.05 µM (0.66 µg

P/L). The average upwelling season phosphate-P concentration in Arcata Bay is 1.8 µM

(25.2 µg P/L) indicating that the daily AWTF phosphate-P discharge may only account for approximately 2.8% of the daily amount of phosphate-P in Arcata Bay. This indicates that the AWTF phosphate-P discharge may not be the cause of elevated concentrations in

Arcata Bay during the upwelling season. This also indicates that mineralization and desorption may be significant sources of phosphate-P in Arcata Bay during the upwelling season. However, the relative contribution of these two mechanisms has not been determined.

Freshwater contributions of phosphate-P to Arcata Bay are more significant with respect to ocean loading than freshwater DIN contributions. During the upwelling season, wastewater phosphate-P contributions to Arcata Bay make up 16% of the total load, while watershed runoff only accounts for approximately 4% of the total load.

During the runoff season, wastewater phosphate-P contributions to Arcata Bay make up

25% of the total load, and watershed runoff accounts for 14%. It should be noted that biological production in Humboldt Bay shows no indication of being phosphorus-limited such that phosphate-P discharges from freshwater sources should not stimulate overproduction in the Bay.

Silicate-Si concentrations are significantly higher in Arcata Bay and South Bay throughout the year indicating significant internal sources exist. Silicate-Si in wastewater discharge has not been determined, however, silicate-Si concentrations are significantly

180 higher in South Bay than in Arcata Bay indicating wastewater discharges do not have a significant impact on silicate-Si concentrations in the Bay since there is no WWTF in

South Bay. Silicate-Si concentrations are also greater during the runoff season than during the upwelling season, indicating high uptake during the upwelling season and increased mineralization during the runoff season which may contribute to significant changes in water column silicate-Si concentrations in the Bay throughout the year.

Budget Surpluses

Approximately 70-85% of the total annual dissolved inorganic nutrient loading to

Humboldt Bay from all sources is unaccounted for by production and uptake, indicating advection of water from the system on ebb tides is the major mechanism of nutrient removal from Humboldt Bay. Evidence in support of nutrient export on ebbing tides includes nutrient concentrations measured at the Bay entrance near low tide that indicate outgoing tidal flows often contain higher nutrient concentrations than incoming tides.

Increased nutrient concentrations in ebb tide water may be due to mineralization of organic matter in the system and nutrient loading from freshwater sources inside the Bay

It should be noted that freshwater sources are minor in comparison to tidal influx indicating that mineralization is a significant source of nutrients in Humboldt Bay. It should also be noted that the scope of this study did not include an estimation of advective nutrient export from the Bay due to the complexity of determining the internal nutrient dynamics that contribute to increased export. Quantifying mineralization of organic matter in the water column was also omitted from the scope of this project for the

181 same reasons, although some consideration of mineralization in sediments is included in sediment flux estimations.

Budget Deficits

Net deficits in the dissolved inorganic nutrient balances indicate uptake is greater than supply and suggest nutrient-limited production inside the Bay. Net deficits occurred for the average annual and upwelling season budget estimates of DIN, phosphate, and silicate in Arcata Bay indicating a high level of productivity with respect to nutrient supply, and the potential for nutrient limitation as opposed to over-production. South

Bay similarly indicates nutrient limitation may contribute to limited production during the upwelling season as net nutrient deficits occur for DIN and phosphate. The greatest deficits occurred with respect to DIN in Arcata Bay during the upwelling season where uptake was approximately 700% greater than supply. This is also an indicator that estimations of uptake may be high and that estimations of loading may be low.

Phytoplankton production represents the largest pool for nutrient uptake in

Humboldt Bay annually, accounting for approximately 57% of all DIN uptake (2,569 Mg

N/yr) and 78% of all phosphate-P uptake (355 Mg P/yr). While estimates of phytoplankton production are greater than all other types of uptake combined for DIN and phosphate-P, it is unclear what the magnitude of the net uptake is with respect to re- mineralization of organic biomass imported from nearshore waters. Therefore, estimations of phytoplankton uptake represent an upper limit of dissolved inorganic nutrient removal from the water column inside the Bay.

182

Denitrification represents the second largest potential pathway for annual DIN uptake in Humboldt Bay, accounting for 17% of all DIN uptake estimated (768 Mg N/yr).

Denitrification represents actual removal from the system making it an important mechanism for nitrogen cycling in the Bay since it will not result in re-mineralized DIN.

Lower N:P ratios in Arcata Bay compared with the Bay entrance indicate denitrification represents a significant DIN removal mechanism in the Bay, supporting estimates of high removal in the budget.

Comparison with Other Systems

Humboldt Bay is a non-eutrophic, upwelling-influenced, nitrogen-limited estuary.

The following is a comparison with two systems; the first is similar to Humboldt Bay and is also considered a healthy non-eutrophic estuary. The second is a highly eutrophic estuary in Southern California impacted by agricultural nutrient runoff and experiencing overproduction of macroalgae.

Comparison of annual biological uptake rates and average ammonium and nitrate concentrations in Humboldt Bay and Tomales Bay (Smith et al., 1991) indicate Humboldt

Bay may be less productive with respect to phytoplankton and macroalgae uptake, though more productive with respect to eelgrass production (Table 61). Denitrification estimates for Humboldt Bay were calculated using findings from Smith et al. (1991) and Dollar et al. (1991); therefore the areal denitrification for both systems are identical and there is no other basis for comparison of this process between the two systems. However, comparisons can be made with respect to nutrient concentrations. Nutrient

183 concentrations in Humboldt Bay appear to be greater during the upwelling season and lower during the runoff season (Table 62). Tomales Bay has a significantly larger watershed that may contribute significantly to higher nutrient concentrations during the runoff season, though limited data are available for Humboldt Bay. Higher nutrient concentrations in Humboldt Bay during the upwelling season may be due to greater influence from upwelling or lower productivity.

Table 61 - Comparison of physical properties and biological uptake in Humboldt Bay and Tomales Bay.

Humboldt Tomales Parameter Bay Bay Bay Area (Mm2) 691 288 Watershed Area (Mm2) 2352 5608 Creek Inputs (Mm3/yr) 3072,3 908 Phytoplankton Uptake (mg N/m2/d) 1004 1278 Macroalgae Uptake (mg N/m2/d) 305,6 638 Eelgrass Uptake (mg N/m2/d) 125,7 68 Denitrification (mg N/m2/d) 301,8,9 468, 259 Total DIN uptake (mg N/m2/d) 144 222-243 1Anderson (2015); 2WBD (2015); 3USGS (2015); 4This study, Harding (1973), Hurst (2009), Hurst (2015), Ryther and Yentsch (1957), Wiyot Tribe Natural Resources Department (2015); 5Schlosser and Eicher (2012); 6Duarte (1992), Pregnall and Rudy (1985); 7Fourqurean et al. (1997); 8Smith et al. (1991); 9Dollar et al. (1991)

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Summer - Summer - Winter - Winter - Location and Humboldt Tomales Humboldt Tomales Constituent Bay1 Bay2 Bay1 Bay2

Outer Bay NO3 (µM) 13 4 11 15

Inner Bay NO3 (µM) 3 1 9 15

Watershed NO3 (µM) 18 1 18 75

Outer Bay NH4 (µM) 4 1 3 3

Inner Bay NH4 (µM) 6 0.5 7 4

Watershed NH4 (µM) 3 0.1 3 1 1Hurst (2009), Hurst (2015), Wiyot Tribe Natural Resources Department (2015); 2Smith et al. (1991)

Upper Newport Bay in Southern California is a eutrophic estuary receiving high nutrient loads from the creek runoff as well as experiencing high nutrient concentrations inside the estuary (Table 63). Comparison of ambient ammonium and nitrate concentrations in the two systems indicates that Humboldt Bay has significantly lower nitrate concentrations during both the upwelling and runoff seasons. Ammonium concentrations are also higher in Upper Newport Bay though not as significant as nitrate, possibly due to the high rate of uptake by macroalgae and phytoplankton. The analysis from Boyle et al. (2004) indicates that tidal channels in Upper Newport Bay may experience greater than 75% cover by macroalgae in the summer and fall.

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Summer - Summer - Winter - Winter - Location and Constituent Humboldt Newport Humboldt Newport Bay1 Bay2 Bay1 Bay2

Tidal Channel NO3 (µM) 13 290 9 140

Creek NO3 (µM) 18 45 18 43

Tidal Channel NH4 (µM) 6 8 7 11

Creek NH4 (µM) 3 9 3 14 1Hurst (2009), Hurst (2015), Wiyot Tribe Natural Resources Department (2015); 2Boyle et al. (2004)

Historical Changes

Humboldt Bay has been the subject of at least five significant nutrient studies since 1962 (other studies have been conducted but remain unpublished). Methods of measuring nutrients have varied, as have sampling locations and time of day with respect to tidal interaction. A series of average nutrient concentrations from various studies conducted since 1962 are presented below (Table 64). Runoff season nitrate and ammonium concentrations inside the Bay and at the Bay entrance have increased since

1980. This may indicate that land use has changed around Humboldt Bay and in the Eel

River watershed. Eel River waters flow northward during the winter runoff season and may influence waters near the Bay entrance. Phosphate and silicate show no indication of increasing at either location or season indicating any land use changes that have resulted in ammonium and nitrate increases have not affected phosphate and silicate. It

186 should be noted that upgrades in wastewater treatment technology in the AWTF and

EWTF may have reduced nutrient loads from these sources such that increases in nutrient concentrations may not be attributable to these sources. It should also be noted that none of these concentrations represents extremely high concentrations and that nutrient levels in Humboldt Bay have remained relatively low during these studies. Recall the Newport

Bay tidal channel nitrate concentration of 290 µM (Table 63).

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Nitrate Ammonium Phosphate Silicate Year Location, Season (µM) (µM) (µM) (µM) 19621 IB, US ND ND 2.2 27.3 19802 IB, US 2.4 1.5 1.8 21.4 19813 IB, US 5.2 15.5 5.7 ND 20064 IB, US 4.7 2.4 3.6 ND 2009-20155 IB, US 3.4 5.8 1.8 23.7 19621 IB, RS ND ND 2.2 27.3 19802 IB, RS 0.8 0.8 1.3 15.2 19813 IB, RS 18.2 5.0 2.9 ND 20064 IB, RS 8.2 6.8 3.0 ND 2009-20155 IB, RS 9.1 6.7 1.5 29.3 19621 OB, US ND ND 2.1 24.4 19802 OB, US 12.6 1.9 1.4 19.2 19813 OB, US 2.6 9.3 2.5 ND 20064 OB, US 18.0 3.1 3.5 ND 2009-20155 OB, US 12.6 3.9 1.4 16.8 19621 OB, RS ND ND 2.1 24.4 19802 OB, RS 0.3 0.0 0.0 2.1 19813 OB, RS 4.3 2.5 2.2 ND 20064 OB, RS 8.9 6.4 2.0 ND 2009-20155 OB, RS 11.1 3.0 1.2 18.1 1Gast (1962); 2Pequegnat and Butler (1981); 3Janeway (1981); 4Tennant (2006); 5Hurst (2009), Hurst (2015), Wiyot Tribe Natural Resources Department (2015), this study

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FUTURE RESEARCH

Estimations of nutrient uptake by phytoplankton, denitrification, and sediment flux used in this study were gathered from literature studies of similar systems that resulted in significant uncertainty. Uncertainty in these estimates can be reduced using more detailed conceptual and numerical models, and site-specific studies of these processes in Humboldt Bay. Estimations of nutrient loading from watershed sources to

Humboldt Bay relied on average nutrient concentrations from a single location and streamflow rates from nearby Little River. These estimates could be significantly improved with additional water quality sampling of the watershed surrounding Humboldt

Bay, and measurement of streamflow rates from creeks emptying directly into Humboldt

Bay. Estimations of nutrient loading to Humboldt Bay from nearshore waters is highly complex and involves the mixing of internal compartments in the Bay, mixing between the Humboldt Bay tidal prism and nearshore waters, various environmental conditions, and various biological processes of uptake and re-mineralization. A combination of hydrodynamic and biodynamic modeling may greatly improve estimation of nutrient contributions to Humboldt Bay from nearshore waters.

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CONCLUSION

Humboldt Bay is a healthy nitrogen-limited estuary where dissolved inorganic nutrients and phytoplankton from nearshore waters are the major influences on productive upwelling season nutrient cycling in the Bay. Limited exchange rates between Arcata Bay and the ocean may reduce ocean nutrient loading by up to 98%, however, nearshore DIN and DIP loading remain more than twice as great as wastewater and watershed runoff sources combined on an annual basis. During the upwelling season, DIN discharge from the AWTF decreases by 75%, significantly reducing potential impacts to the Bay during this period of high productivity. All estimations of individual biological DIN and DIP uptake processes in Arcata Bay are greater than the

AWTF DIN and DIP discharge further supporting the conclusion that wastewater nutrient discharge has little or no significant impact on biological productivity in Arcata Bay compared with other nutrient sources.

190

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APPENDIX A - SAMPLE SITE COORDINATES

Sample site coordinates in UTM zone 10 projection.

Sample Site Longitude Latitude Wiyot Tribe Sample Sites Hookton Slough (HS) 396750 4503670 Bay Entrance (BE) 397065 4512670 Samoa Channel (SC) 400915 4519100 Mad River Slough (MRS) 403110 4524445 Indian Island (II) 402390 4518855 Professor Hurst's Sample Sites Mad River Slough (MRS) 403110 4524445 McDaniel's Slough (MDS) 407260 4523880 Butcher's Slough (BS) 408080 4523385 Freshwater Slough (FWS) 406418 4515718 Eureka Channel (EC) 402040 4517895 Jacoby Creek (JC) 409790 4521300 Elk River (ER) 399158 4512386 Author's Sample Sites South Bay (SB) 396570 4510875 Bay Entrance (BE) 397065 4512670 Coast Guard Station (CG) 397500 4513390 Main Channel (MC) 399925 4517475 Samoa Channel (SC) 400915 4519100 Mad River Slough Channel (MRC) 403355 4521930 Bird Island (BI) 403195 4519970 Arcata Channel (AC) 405510 4521285 Indian/Woodley Channel (I/W) 403935 4519685 Indian Island (II) 402390 4518855

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APPENDIX B - WATER QUALITY DATA

203

South Bay (SB) entrance station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/03/22 10:40 Low 10.39 33.12 8.84 0.38 31.75 15.60 1.43 8.29 0.29 2014/03/22 16:54 High 9.34 33.87 7.36 0.04 29.21 24.04 1.93 4.43 0.20 2014/06/03 09:38 Low 13.50 34.05 7.74 0.57 21.83 3.32 1.33 7.05 0.19 2014/06/03 16:38 High 10.48 33.92 11.12 4.52 14.47 4.87 0.37 1.75 0.16 2014/06/16 08:05 Low 13.12 34.31 7.44 2.07 26.68 8.48 1.43 5.10 0.31 2014/06/16 14:49 High 9.86 34.21 8.52 10.79 26.23 13.54 1.07 2.77 0.48 2014/07/17 09:30 Low 13.56 33.89 8.05 1.70 16.23 4.26 1.20 7.19 0.24 2014/07/17 15:45 High 11.08 33.79 9.42 8.29 10.12 8.54 0.92 2.88 0.21 2014/08/13 07:11 Low 14.00 34.04 7.62 1.90 10.12 8.54 0.92 2.88 0.21 2014/08/13 13:45 High 12.51 33.99 11.54 6.54 11.22 3.36 1.09 7.51 0.19 2014/09/12 07:35 Low 13.94 34.01 7.48 2.10 24.91 14.25 1.37 7.01 0.35 2014/09/12 15:37 High 13.10 33.90 9.19 4.00 18.68 17.03 1.47 4.40 0.23 2014/10/12 08:08 Low 12.68 33.67 0.83 19.86 5.59 1.00 7.24 0.43 2014/10/12 13:49 High 12.12 33.69 1.76 19.14 7.47 1.24 4.48 0.39 2014/11/02 13:00 Low 13.64 33.48 8.32 0.91 8.42 17.97 1.41 4.96 0.33 2014/11/02 07:51 High 13.99 33.30 8.75 1.05 15.23 12.70 1.26 7.06 0.41 2014/12/30 12:41 Low 10.13 31.15 9.24 0.78 27.80 2.09 0.72 7.09 0.52 2014/12/31 06:58 High 0.25 17.02 8.79 1.32 3.50 0.20 2015/02/01 15:26 Low 10.80 31.10 6.96 0.70 18.52 8.00 0.86 0.82 0.23 2015/02/01 08:31 High 10.80 31.10 6.96 0.70 18.52 8.00 0.86 0.82 0.23 2015/02/10 09:08 Low 12.70 26.90 7.38 0.43 32.60 7.50 0.81 5.10 0.20 2015/02/10 14:50 High 12.80 27.70 8.78 0.20 25.37 3.38 0.67 1.46 0.09

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Bay Entrance (BE) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 08:00 Low 9.91 33.30 10.00 0.66 13.74 9.66 1.23 4.88 0.24 2014/01/20 12:55 High 9.92 33.46 10.50 0.32 15.00 13.71 1.42 4.22 0.27 2014/03/22 10:50 Low 10.39 32.37 8.90 0.26 29.01 16.57 1.61 5.98 0.31 2014/03/22 17:01 High 9.58 33.86 7.80 0.26 28.84 23.53 1.95 3.22 0.19 2014/06/03 09:50 Low 13.27 33.97 7.86 5.22 25.15 8.65 1.58 6.41 0.29 2014/06/03 16:47 High 10.49 33.94 10.58 7.71 23.28 7.27 0.55 2.69 0.22 2014/06/16 08:20 Low 13.02 34.33 7.38 6.62 32.90 13.21 1.74 4.35 0.39 2014/06/16 14:57 High 9.62 34.20 8.10 10.52 21.95 13.34 1.19 2.73 0.49 2014/07/17 09:40 Low 14.40 33.95 8.01 4.16 22.23 8.30 2.13 9.37 0.33 2014/07/17 15:55 High 12.29 33.76 12.16 7.71 0.74 0.17 0.21 2.17 0.01 2014/08/13 07:24 Low 14.70 34.16 7.99 4.37 12.84 3.18 1.07 4.83 0.19 2014/08/13 13:55 High 12.35 33.92 11.41 6.32 1.83 2.91 0.48 3.06 0.11 2014/09/12 07:50 Low 14.20 34.06 8.59 3.02 22.33 14.66 1.45 4.51 0.28 2014/09/12 15:47 High 13.51 33.86 10.80 7.79 14.40 16.22 1.42 3.51 0.09 2014/10/12 08:19 Low 12.36 33.68 1.88 18.96 4.73 0.90 4.90 0.41 2014/10/12 13:57 High 11.81 33.70 1.45 18.14 4.49 1.22 4.16 0.37 2014/11/02 13:07 Low 13.94 33.36 8.80 1.14 7.89 15.80 1.31 4.54 0.31 2014/11/02 08:00 High 14.28 33.04 8.79 1.36 14.66 13.71 1.29 5.12 0.38 2014/12/30 12:49 Low 10.79 30.37 8.91 0.65 29.67 3.02 0.80 5.97 0.55 2014/12/31 07:12 High 11.10 0.00 0.16 15.67 10.20 1.57 2.48 0.24 2015/02/01 15:35 Low 12.10 30.20 8.10 1.62 17.97 8.20 1.06 1.38 0.21 2015/02/01 08:45 High 11.30 30.60 7.93 0.95 17.16 10.62 0.99 0.90 0.23 2015/02/10 09:17 Low 12.90 25.10 7.47 0.49 43.78 14.05 1.40 7.96 0.34 2015/02/10 15:24 High 12.80 27.70 8.39 0.28 26.60 6.71 0.83 3.76 0.18

205

Coast Guard (CG) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 08:10 Low 9.89 33.25 10.76 0.55 13.59 9.22 1.19 6.72 0.23 2014/01/20 13:02 High 9.94 33.46 10.30 0.66 14.37 13.00 1.31 3.60 0.25 2014/03/22 11:00 Low 11.06 31.74 8.90 0.16 30.34 15.60 1.53 8.79 0.32 2014/03/22 17:10 High 9.30 33.92 7.44 0.30 29.89 24.79 1.98 3.92 0.20 2014/06/03 09:57 Low 14.23 34.02 7.40 1.28 27.23 6.82 1.50 7.37 0.28 2014/06/03 16:55 High 10.30 33.95 10.31 8.14 18.76 8.04 0.56 2.45 0.21 2014/06/16 12:49 Low 14.50 34.43 7.01 3.98 34.97 10.03 1.71 5.36 0.34 2014/06/16 15:02 High 9.45 34.21 7.55 11.60 28.91 17.49 1.45 4.33 0.57 2014/07/17 09:45 Low 15.00 34.14 7.62 2.98 23.90 5.57 1.52 7.56 0.26 2014/07/17 16:00 High 12.37 33.76 12.37 5.13 0.73 0.08 0.17 2.09 0.00 2014/08/13 07:30 Low 15.29 34.25 7.50 3.68 17.28 2.97 1.28 6.12 0.22 2014/08/13 14:00 High 12.13 33.95 11.10 6.73 1.16 3.70 0.53 2.77 0.11 2014/09/12 08:00 Low 14.69 34.14 7.83 3.21 25.96 14.30 1.42 6.13 0.34 2014/09/12 15:53 High 13.38 33.88 10.35 8.47 15.25 16.63 1.41 3.30 0.14 2014/10/12 08:26 Low 12.58 33.67 1.99 19.62 5.01 0.95 5.61 0.40 2014/10/12 14:02 High 11.65 33.71 1.19 18.30 7.63 1.38 5.39 0.39 2014/11/02 13:14 Low 13.85 33.39 8.59 1.18 8.29 16.57 1.35 3.57 0.29 2014/11/02 08:06 High 14.40 32.81 8.65 1.30 18.26 14.58 1.42 7.04 0.41 2014/12/30 12:56 Low 10.54 29.54 8.97 0.64 34.88 4.24 0.95 6.27 0.53 2014/12/31 07:20 High 0.19 15.91 6.14 1.90 2.20 0.22 2015/02/01 15:42 Low 11.30 30.60 7.86 0.95 17.02 10.66 1.04 1.17 0.23 2015/02/01 08:55 High 11.30 30.60 7.86 0.95 17.02 10.66 1.04 1.17 0.23 2015/02/10 09:25 Low 13.00 25.70 7.40 0.34 40.45 10.68 1.16 7.39 0.29 2015/02/10 15:38 High 12.90 28.00 8.40 0.10 19.35 3.67 0.65 1.86 0.09

206

Main Channel (MC) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 08:25 Low 9.89 32.99 0.90 13.15 6.30 1.05 5.38 0.19 2014/01/20 13:17 High 9.95 33.39 10.20 0.69 14.16 11.11 1.24 4.54 0.25 2014/03/22 11:15 Low 11.47 30.82 8.45 0.46 27.69 10.08 1.28 7.44 0.36 2014/03/22 17:25 High 10.88 32.67 8.94 0.21 30.19 19.54 1.73 6.30 0.31 2014/06/03 10:09 Low 16.18 34.10 6.42 0.67 31.97 4.06 1.67 8.66 0.26 2014/06/03 17:10 High 11.43 33.96 9.79 8.22 27.39 7.85 0.77 3.21 0.30 2014/06/16 08:41 Low 16.32 34.64 6.38 1.34 40.00 5.52 1.83 6.35 0.27 2014/06/16 15:16 High 10.07 34.23 7.50 9.93 29.85 18.29 1.42 2.98 0.52 2014/07/17 10:00 Low 16.69 34.39 6.66 1.58 32.41 3.14 1.87 8.41 0.26 2014/07/17 16:10 High 12.50 33.78 11.61 7.63 1.03 0.07 0.22 2.24 0.00 2014/08/13 07:43 Low 16.86 34.49 6.36 1.89 28.59 3.04 1.76 8.26 0.26 2014/08/13 14:15 High 12.54 33.92 12.10 6.41 0.26 1.25 0.32 2.39 0.06 2014/09/12 08:15 Low 16.27 34.32 7.06 3.31 33.40 14.81 1.75 6.29 0.34 2014/09/12 16:06 High 13.83 33.95 9.17 4.54 17.18 22.54 1.43 4.32 0.22 2014/10/12 08:39 Low 14.58 33.55 1.39 24.72 9.73 1.70 7.52 0.43 2014/10/12 14:14 High 11.85 33.69 1.48 18.80 7.20 1.39 5.27 0.40 2014/11/02 13:28 Low 14.13 33.24 8.65 1.09 9.24 10.51 0.96 5.03 0.29 2014/11/02 08:18 High 14.82 32.16 8.28 1.26 27.46 15.04 1.51 8.15 0.46 2014/12/30 13:09 Low 10.00 27.70 9.17 0.73 46.11 10.00 1.03 7.70 0.50 2014/12/31 07:32 High 0.26 17.01 8.55 1.98 2.08 0.24 2015/02/01 15:56 Low 11.30 30.90 7.88 0.99 15.31 10.75 1.04 0.55 0.25 2015/02/01 09:10 High 11.30 30.90 7.88 0.99 15.31 10.75 1.04 0.55 0.25 2015/02/10 09:38 Low 13.00 24.10 6.96 0.45 52.65 13.56 1.36 10.24 0.36 2015/02/10 15:53 High 13.00 26.40 8.14 0.50 36.60 9.33 1.04 5.86 0.22

207

Samoa Channel (SC) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 08:33 Low 9.92 32.97 11.15 0.23 13.54 6.35 1.08 6.16 0.19 2014/01/20 13:25 High 9.97 33.32 10.31 0.66 13.69 10.10 1.20 5.17 0.24 2014/03/22 11:30 Low 11.52 30.70 8.39 0.81 28.44 10.97 1.31 7.17 0.36 2014/03/22 17:37 High 11.54 31.93 8.89 0.16 30.35 15.52 1.58 6.71 0.34 2014/06/03 10:18 Low 16.66 34.15 6.40 0.61 37.65 3.17 1.68 8.80 0.33 2014/06/03 17:18 High 12.88 33.96 8.89 8.02 21.15 6.29 0.91 5.15 0.27 2014/06/16 08:47 Low 16.91 34.71 6.07 1.19 41.24 4.16 1.87 6.12 0.24 2014/06/16 15:24 High 10.81 34.26 7.41 9.23 36.60 17.88 1.88 4.39 0.54 2014/07/17 10:05 Low 17.10 34.46 6.45 1.33 33.93 2.79 1.84 8.41 0.24 2014/07/17 16:18 High 12.88 33.81 11.10 7.75 2.30 0.30 0.35 2.51 0.03 2014/08/13 07:51 Low 17.51 34.59 6.06 1.90 32.63 2.79 1.95 7.95 0.26 2014/08/13 14:20 High 13.26 33.99 11.40 6.43 1.69 1.41 0.44 3.07 0.08 2014/09/12 08:25 Low 16.92 34.41 7.00 2.47 34.97 15.06 1.82 5.59 0.29 2014/09/12 16:14 High 13.77 33.95 9.32 4.31 17.78 15.68 1.49 3.18 0.18 2014/10/12 08:46 Low 15.10 33.52 1.28 26.84 10.30 1.13 7.12 0.41 2014/10/12 14:22 High 11.98 33.71 2.24 19.42 8.09 1.90 6.17 0.36 2014/11/02 13:35 Low 14.34 32.99 8.43 0.57 12.31 17.62 1.33 5.37 0.32 2014/11/02 08:27 High 14.96 31.87 8.43 1.41 31.81 15.63 1.62 8.60 0.48 2014/12/30 13:17 Low 10.03 27.81 9.10 0.77 45.63 8.74 1.39 9.06 0.57 2014/12/31 07:41 High 0.40 21.38 5.85 2.33 4.05 0.34 2015/02/01 16:05 Low 11.50 30.90 7.72 1.27 15.17 10.26 1.07 1.28 0.25 2015/02/01 09:20 High 11.50 30.90 7.72 1.27 15.17 10.26 1.07 1.28 0.25 2015/02/10 09:45 Low 13.20 24.60 6.73 0.55 49.91 13.87 1.47 10.51 2015/02/10 16:03 High 13.00 26.40 7.91 0.48 39.31 10.20 1.14 7.11

208

Mad River Slough Channel (MRC) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 09:15 Low 8.98 32.64 11.18 0.30 8.36 1.20 0.74 4.76 0.06 2014/01/20 14:00 High 10.08 32.98 10.51 0.71 13.32 6.10 1.08 5.79 0.19 2014/03/22 11:45 Low 11.66 29.94 8.70 0.13 26.43 6.73 1.22 7.11 0.34 2014/03/22 17:29 High 11.69 31.14 8.65 0.46 29.91 12.58 1.42 7.18 0.37 2014/06/03 10:30 Low 17.57 34.31 5.66 0.39 39.05 1.37 1.83 8.47 0.24 2014/06/03 17:31 High 17.56 34.20 6.78 3.37 35.76 3.23 1.74 8.76 0.31 2014/06/16 08:57 Low 17.38 34.90 5.65 1.08 45.30 2.43 2.24 6.07 0.20 2014/06/16 15:36 High 15.28 34.50 6.95 3.30 29.71 6.62 1.22 7.36 0.54 2014/07/17 10:20 Low 18.30 34.81 5.81 1.53 45.75 2.60 2.33 7.67 0.27 2014/07/17 16:33 High 14.95 34.11 7.78 10.56 22.23 5.00 1.44 6.87 0.26 2014/08/13 08:01 Low 18.44 34.89 5.53 2.09 43.27 2.71 2.45 7.93 0.26 2014/08/13 14:30 High 15.00 34.17 8.63 4.30 15.30 3.12 1.18 5.94 0.21 2014/09/12 08:38 Low 17.67 34.66 5.95 1.02 40.07 10.11 2.18 5.42 0.25 2014/09/12 16:24 High 15.32 34.13 8.68 4.97 24.51 13.82 1.66 4.31 0.24 2014/10/12 08:58 Low 15.72 33.45 0.81 32.60 11.02 1.62 6.93 0.39 2014/10/12 14:32 High 13.80 33.61 1.03 22.72 14.46 2.12 6.04 0.38 2014/11/02 13:48 Low 15.03 32.11 8.12 1.17 23.71 18.83 1.44 7.93 0.43 2014/11/02 08:38 High 15.10 31.60 9.21 1.74 36.02 18.32 2.09 7.50 0.43 2014/12/30 13:34 Low 9.34 25.11 9.44 0.91 62.35 7.50 1.21 11.43 0.73 2014/12/31 07:53 High 0.55 32.36 6.30 2.18 4.19 0.47 2015/02/01 16:17 Low 13.20 28.70 8.76 1.42 29.17 4.93 1.27 1.76 0.09 2015/02/01 09:36 High 12.00 30.20 7.11 1.32 19.04 7.87 1.02 1.21 0.20 2015/02/10 09:57 Low 12.90 22.90 6.72 0.95 60.33 18.80 1.90 13.35 0.61 2015/02/10 16:14 High 13.30 24.60 7.74 0.71 50.39 13.76 1.49 10.86 0.40

209

Bird Island (BI) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 09:43 Low 9.34 32.79 11.13 0.49 13.10 4.37 1.02 7.23 0.17 2014/01/20 14:10 High 10.05 33.07 10.20 0.77 13.66 7.14 1.12 6.23 0.20 2014/03/22 12:05 Low 11.52 30.34 8.35 1.09 27.51 7.79 1.19 7.83 0.34 2014/03/22 18:12 High 11.71 31.35 8.76 0.61 31.51 13.21 1.45 7.09 0.35 2014/06/03 10:45 Low 17.30 34.26 5.50 0.63 34.89 1.53 1.69 7.80 0.20 2014/06/03 17:48 High 14.83 34.02 7.36 1.96 28.27 6.49 1.52 8.33 0.29 2014/06/16 09:10 Low 16.93 34.80 5.93 1.56 44.77 3.19 2.01 10.71 0.32 2014/06/16 15:53 High 12.55 34.32 7.55 5.62 30.42 12.52 1.41 6.08 0.56 2014/07/17 10:30 Low 17.71 34.61 5.83 1.47 38.96 2.06 2.05 7.13 0.22 2014/07/17 16:37 High 13.69 33.92 9.15 6.08 13.58 3.90 0.93 4.87 0.20 2014/08/13 08:12 Low 18.08 34.71 5.78 1.80 37.26 2.79 2.17 8.80 0.27 2014/08/13 14:40 High 13.53 33.99 10.81 5.72 2.28 1.41 0.53 3.38 0.10 2014/09/12 08:50 Low 17.40 34.52 6.32 1.80 39.62 11.25 2.03 6.44 0.29 2014/09/12 16:35 High 14.86 34.05 9.27 6.33 22.04 14.68 1.52 4.47 0.18 2014/10/12 09:13 Low 15.63 33.47 1.13 30.76 9.62 1.38 8.56 0.37 2014/10/12 14:43 High 12.89 33.67 1.09 20.40 14.46 2.04 6.22 0.35 2014/11/02 13:59 Low 14.73 32.56 8.53 1.41 18.29 16.31 1.38 7.24 0.37 2014/11/02 08:49 High 15.03 31.50 8.56 1.04 35.98 16.55 1.66 9.25 0.48 2014/12/30 13:46 Low 9.89 26.88 9.09 0.57 49.80 10.09 1.42 10.11 0.53 2014/12/31 08:06 High 0.49 25.63 7.44 2.25 5.12 0.39 2015/02/01 16:27 Low 13.00 29.00 8.25 1.76 26.00 4.86 1.09 2.95 0.16 2015/02/01 09:48 High 11.80 30.60 7.38 1.35 16.84 8.72 0.97 1.09 0.22 2015/02/10 10:09 Low 12.90 24.20 6.88 0.70 53.91 15.28 1.54 5.75 0.46 2015/02/10 16:23 High 13.20 25.00 7.91 0.81 47.47 12.83 1.37 9.29 0.39

210

Arcata Channel (AC) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 09:53 Low 8.85 32.45 10.31 0.62 10.80 3.75 0.90 5.20 0.13 2014/01/20 14:30 High 10.24 32.84 11.18 0.85 12.72 4.62 1.01 5.87 0.16 2014/03/22 12:15 Low 10.67 29.61 8.05 0.82 26.67 5.50 1.18 8.60 0.30 2014/03/22 18:29 High 11.73 30.88 8.54 0.36 29.77 11.30 1.35 7.93 0.38 2014/06/03 10:56 Low 17.03 34.27 5.21 0.60 36.76 0.85 1.79 10.09 0.18 2014/06/03 18:00 High 16.20 34.09 6.58 1.59 40.29 4.34 1.99 14.66 0.35 2014/06/16 09:18 Low 16.85 35.07 5.05 1.42 43.95 0.75 1.97 4.81 0.09 2014/06/16 16:04 High 14.99 34.47 7.12 3.42 35.85 9.32 1.73 6.51 0.40 2014/07/17 10:40 Low 18.06 34.80 5.11 2.47 46.69 1.49 2.24 6.37 0.19 2014/07/17 16:50 High 15.32 34.15 7.54 3.20 23.78 4.93 1.51 7.52 0.27 2014/08/13 08:25 Low 18.05 34.89 5.06 2.29 44.85 3.23 2.22 8.38 0.31 2014/08/13 14:48 High 14.81 34.14 8.85 5.06 12.90 3.01 1.03 5.96 0.21 2014/09/12 09:02 Low 17.34 34.59 5.88 1.63 41.66 11.84 2.12 6.96 0.28 2014/09/12 16:46 High 14.87 34.08 8.71 3.22 24.52 9.93 1.73 5.31 0.23 2014/10/12 09:23 Low 15.50 33.44 1.60 36.46 13.76 1.68 8.52 0.38 2014/10/12 14:50 High 14.31 33.59 1.10 24.21 14.40 2.06 7.32 0.41 2014/11/02 14:11 Low 15.07 31.91 8.02 0.72 26.27 14.42 1.44 9.42 0.43 2014/11/02 08:59 High 15.27 30.94 8.72 1.60 42.94 18.34 1.69 9.60 0.49 2014/12/30 14:00 Low 9.52 25.96 9.27 0.64 56.60 9.01 1.60 11.35 0.57 2014/12/31 08:18 High 0.57 34.06 3.84 2.04 6.89 0.49 2015/02/01 16:37 Low 13.50 28.40 7.71 2.17 32.07 7.44 1.36 8.80 0.24 2015/02/01 10:00 High 12.10 29.90 6.95 1.51 20.91 7.32 1.09 1.92 0.23 2015/02/10 10:21 Low 12.50 23.10 6.88 0.74 60.08 17.25 1.56 11.42 0.45 2015/02/10 16:32 High 13.20 24.50 7.36 1.06 52.14 14.52 1.57 12.21 0.48

211

Indian/Woodley Channel (I/W) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 10:15 Low 9.37 32.69 10.77 0.38 14.02 4.14 1.14 11.10 0.24 2014/01/20 14:47 High 10.13 33.06 10.84 1.96 14.18 7.28 1.15 6.30 0.20 2014/03/22 12:30 Low 11.80 29.98 8.35 0.66 29.00 7.83 1.17 8.20 0.39 2014/03/22 18:41 High 12.39 30.90 9.01 0.55 30.39 11.64 1.37 7.49 0.37 2014/06/03 11:06 Low 17.52 34.30 6.19 0.74 32.95 1.90 1.55 6.47 0.21 2014/06/03 18:13 High 16.08 34.07 7.23 1.55 30.56 4.62 1.66 9.03 0.27 2014/06/16 09:27 Low 17.70 35.06 5.89 1.52 43.49 1.98 1.83 5.82 0.18 2014/06/16 16:17 High 14.05 34.39 7.65 5.68 31.73 10.52 1.52 5.53 0.40 2014/07/17 10:52 Low 18.38 34.75 6.36 1.00 36.01 1.30 1.98 5.40 0.16 2014/07/17 17:00 High 34.01 8.61 5.03 17.66 4.72 1.21 5.84 0.26 2014/08/13 08:33 Low 18.46 34.92 5.28 1.66 31.20 0.55 2.06 4.03 0.10 2014/08/13 15:00 High 14.75 34.16 9.46 5.38 11.58 2.69 1.01 5.40 0.20 2014/09/12 09:30 Low 17.59 34.57 6.57 1.10 34.85 8.64 2.03 5.32 0.17 2014/09/12 16:55 High 15.68 34.15 8.32 3.33 27.14 11.59 1.62 5.80 0.28 2014/10/12 09:34 Low 15.65 33.45 1.69 27.55 8.24 1.45 6.59 0.34 2014/10/12 14:59 High 13.78 33.62 0.60 22.29 11.09 1.82 6.53 0.35 2014/11/02 14:21 Low 14.82 32.32 8.25 0.64 20.51 14.01 1.41 7.89 0.40 2014/11/02 09:10 High 14.99 31.18 10.43 1.40 29.56 13.97 1.67 5.55 0.39 2014/12/30 14:11 Low 9.79 26.15 9.38 0.90 52.80 8.09 1.42 9.29 0.48 2014/12/31 08:29 High 0.57 31.29 6.00 1.93 4.60 0.47 2015/02/01 16:47 Low 13.20 28.90 8.01 2.37 22.44 1.82 0.92 1.37 0.08 2015/02/01 10:15 High 11.90 30.30 7.42 1.74 18.34 8.22 1.03 1.91 0.26 2015/02/10 10:28 Low 13.00 24.20 6.93 1.10 54.62 13.84 1.49 10.30 0.40 2015/02/10 16:40 High 13.20 24.40 7.80 0.85 51.49 14.42 1.40 10.26 0.42

212

Indian Island (II) station water quality data. Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) Tide (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/01/20 10:37 Low 9.56 32.89 10.70 0.50 13.12 5.14 1.05 5.92 0.18 2014/01/20 14:58 High 10.62 33.02 11.38 0.61 13.03 6.36 1.08 5.72 0.19 2014/03/22 12:40 Low 11.66 29.98 8.26 0.64 29.98 9.14 1.21 8.29 0.41 2014/03/22 18:51 High 11.74 31.42 8.70 0.48 34.45 13.55 1.46 7.18 0.36 2014/06/03 11:17 Low 17.14 34.21 6.29 0.63 32.09 2.41 1.63 7.71 0.23 2014/06/03 18:24 High 14.80 33.99 7.75 3.12 31.92 6.42 1.51 11.95 0.33 2014/06/16 09:36 Low 16.74 34.70 5.98 1.58 40.66 4.50 1.88 7.58 0.27 2014/06/16 16:28 High 12.54 34.33 7.45 6.78 33.05 11.13 1.59 5.23 0.38 2014/07/17 11:05 Low 17.52 34.54 6.16 1.32 33.67 2.10 1.93 7.82 0.21 2014/07/17 17:10 High 14.77 34.06 8.77 1.23 17.60 3.70 1.13 6.03 0.24 2014/08/13 08:40 Low 17.10 34.55 6.09 6.10 30.26 2.27 1.90 7.32 0.22 2014/08/13 15:10 High 14.30 34.08 10.15 7.09 8.60 1.91 0.77 4.66 0.16 2014/09/12 09:42 Low 17.24 34.48 7.26 2.83 32.92 12.67 2.01 5.21 0.20 2014/09/12 17:04 High 15.27 34.13 8.78 3.89 24.46 20.04 1.59 5.22 0.25 2014/10/12 09:44 Low 15.51 33.48 9.79 0.96 28.02 11.11 1.31 5.10 0.41 2014/10/12 15:07 High 13.29 33.65 11.51 1.28 20.98 14.45 1.80 7.50 0.39 2014/11/02 14:28 Low 14.60 32.54 8.33 1.14 17.76 20.22 1.45 6.29 0.39 2014/11/02 09:19 High 15.32 31.80 9.37 1.68 28.88 23.76 1.58 7.71 0.44 2014/12/30 14:23 Low 10.21 26.73 9.33 1.10 50.12 6.40 1.45 8.27 0.51 2014/12/31 08:40 High 8.50 0.51 33.44 15.86 1.31 5.62 0.47 2015/02/01 17:04 Low 13.00 29.10 8.20 1.87 23.06 3.40 1.01 2.03 0.14 2015/02/01 10:30 High 11.70 30.70 7.55 1.31 16.36 9.46 1.05 1.62 0.29 2015/02/10 10:38 Low 13.00 24.00 7.10 0.75 54.75 14.27 1.46 10.23 0.44 2015/02/10 16:49 High 14.10 24.30 8.74 1.22 52.63 13.63 1.49 10.23 0.46

213

Mad River Slough (MRS) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/10/13 11:44 15.90 33.30 28.00 4.00 2.20 7.20 0.10 2012/10/20 11:07 15.70 32.70 1.60 24.60 4.20 2.10 5.90 0.10 2012/10/27 16:10 14.41 31.65 2.21 25.90 5.80 2.60 4.70 0.10 2012/11/03 12:03 14.86 32.22 2.12 23.00 4.50 1.90 7.60 0.20 2012/11/17 12:12 12.84 31.95 1.70 23.40 5.10 1.80 7.40 0.20 2012/12/01 11:56 12.71 27.64 1.90 40.40 11.20 1.80 11.50 0.40 2012/12/15 10:58 8.91 28.11 1.57 43.20 9.80 1.60 10.70 0.40 2012/12/29 10:10 8.21 22.58 1.28 62.50 15.90 1.90 13.00 0.50 2013/01/14 12:18 7.39 28.09 2.04 46.10 12.70 1.60 6.70 0.30 2013/01/26 14:05 9.84 28.47 9.34 1.98 39.00 9.50 1.50 5.30 0.20 2013/02/09 13:32 8.86 29.55 9.49 3.47 24.80 3.80 1.20 4.20 0.10 2013/02/23 11:40 9.46 30.75 9.41 3.77 16.10 1.20 0.90 3.40 0.00 2013/03/10 2013/04/13 14:00 13.90 30.37 2.49 29.60 2.90 1.80 6.60 0.10 2013/04/27 12:30 14.00 33.20 4.20 27.50 3.20 1.90 7.50 0.10 2013/05/11 10:45 16.04 33.40 8.85 8.61 14.60 0.00 1.50 6.00 0.00 2013/05/26 13:55 18.63 34.10 9.36 6.15 22.10 0.80 1.90 5.00 0.00 2013/06/08 11:43 17.94 32.88 7.46 8.14 2.00 1.50 2.00 0.00 2013/06/22 14:40 19.74 34.01 8.01 9.35 6.20 0.20 3.70 2.70 0.00 2013/07/06 13:00 20.20 34.30 7.35 5.93 3.80 0.00 2.80 2.60 0.00 2013/07/20 11:57 17.33 34.78 7.92 6.33 1.90 0.00 2.70 2.40 0.00 2013/08/16 13:00 22.29 34.82 8.00 2.93 4.80 0.40 3.00 2.80 0.00

214

Mad River Slough (MRS) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/08/24 18:10 18.58 34.55 7.42 3.90 24.30 0.70 2.80 3.30 0.00 2013/09/07 15:34 20.70 34.35 7.23 3.83 24.60 0.20 2.80 2.70 0.00 2013/09/20 18:05 18.33 34.16 7.66 1.38 25.20 0.80 3.10 2.70 0.00 2013/10/05 15:25 16.00 32.36 8.73 1.86 24.80 0.80 2.10 3.10 0.00 2013/10/19 16:35 13.92 33.10 8.36 1.09 21.60 1.70 1.90 3.70 0.00 2013/11/08 15:15 12.80 32.60 10.16 0.90 17.50 2.70 1.50 3.60 0.00 2013/11/23 17:10 10.36 33.04 10.10 1.15 19.30 2.00 1.30 5.40 0.10 2013/12/07 13:05 6.48 32.85 10.54 1.07 16.90 2.50 1.20 4.20 0.00 2013/12/21 16:50 7.27 32.91 10.76 1.38 14.80 3.20 1.10 3.80 0.00 2014/01/15 14:10 9.04 32.44 10.24 0.59 15.90 3.20 1.10 5.50 0.10 2014/02/02 12:45 9.67 32.76 10.04 1.12 15.90 3.00 1.10 4.40 0.10 2014/02/15 12:20 12.32 31.67 9.49 1.74 26.00 5.80 1.30 13.50 0.40 2014/03/02 17:48 13.23 27.79 1.42 36.10 8.60 1.80 8.50 0.60 2014/03/15 13:26 14.15 26.96 8.91 1.55 33.20 6.80 1.40 9.70 0.50 2014/03/29 12:00 12.85 29.51 8.85 0.87 25.90 5.00 1.30 5.80 0.20 2014/04/12 11:00 15.08 30.21 8.53 1.32 21.40 2.30 1.20 4.70 0.10 2014/04/26 11:00 15.45 31.55 7.95 1.64 19.40 3.10 1.60 4.10 0.20 2014/05/10 13:36 17.90 32.57 6.72 1.33 29.40 2.30 2.20 5.00 0.20 2014/05/26 12:45 18.54 33.80 7.35 0.49 30.20 1.90 1.80 4.80 0.20 2014/06/14 14:31 18.44 34.72 7.93 0.44 44.80 3.29 2.09 8.27 0.24 2014/06/28 14:43 19.35 34.75 6.96 2.10 40.50 2.12 2.10 9.45 0.26 2014/07/26 10:49 19.66 34.90 6.36 2.50 46.10 1.55 2.41 6.39 0.22

215

216

McDaniel's Slough (MDS) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/10/13 11:14 16.40 32.80 36.36 4.74 3.32 7.50 0.20 2012/10/20 10:30 16.50 31.70 3.43 41.32 7.08 3.77 10.39 0.34 2012/11/03 11:15 15.69 30.70 3.49 41.88 10.12 3.24 10.12 0.36 2012/11/17 16:26 13.28 30.10 3.42 31.81 5.80 2.12 5.90 0.17 2012/12/01 10:19 12.77 14.10 2.28 69.23 30.94 3.34 22.03 0.83 2012/12/15 12:15 7.94 24.70 1.77 60.58 15.88 1.41 12.12 0.42 2012/12/29 13:10 8.00 21.50 0.45 78.68 61.80 1.49 11.81 0.60 2013/01/14 13:53 6.53 24.20 2.10 68.42 19.96 1.48 9.46 0.33 2013/01/26 13:09 10.13 26.20 9.16 0.94 50.10 12.73 1.30 7.28 0.19 2013/02/09 12:22 8.56 25.60 1.92 43.06 7.84 1.10 5.85 0.09 2013/02/23 11:10 9.64 27.90 4.19 33.36 4.88 0.92 5.05 0.08 2013/03/10 2.83 70.40 4.98 1.44 5.88 0.08 2013/04/13 16:00 15.51 27.00 5.21 24.53 2.38 1.59 6.09 0.05 2013/04/27 14:41 14.93 29.80 3.68 31.53 4.38 1.84 10.48 0.20 2013/05/11 11:49 15.73 25.40 5.01 4.81 27.86 9.75 2.15 12.59 0.36 2013/05/26 15:20 20.20 33.70 7.88 6.35 21.52 0.64 2.03 4.05 0.00 2013/06/08 13:07 20.40 32.00 6.23 6.48 22.40 1.10 0.99 3.24 0.00 2013/06/22 15:40 21.83 33.00 5.56 5.04 13.50 0.43 6.81 4.50 0.00 2013/07/06 14:40 23.10 29.70 6.56 3.50 21.20 0.11 2.70 3.15 0.00 2013/07/20 14:26 19.23 34.60 5.49 3.76 18.10 0.71 2.04 4.52 0.00 2013/08/16 10:12 22.63 34.60 4.29 3.68 28.60 0.68 1.92 5.07 0.00 2013/08/24 16:05 20.24 34.40 6.36 2.20 29.50 0.55 2.23 3.76 0.00 2013/09/07 15:10 21.99 34.50 5.13 3.31 46.90 0.41 3.17 4.39 0.00 2013/09/20 16:00 17.73 32.40 7.29 1.59 37.00 1.34 1.63 3.37 0.00

217

Freshwater Slough (FWS) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/10/13 13:37 16.20 25.20 52.64 8.84 1.27 3.31 0.12 2012/10/20 11:51 15.50 19.10 2.55 111.56 11.79 1.49 5.17 0.16 2012/10/27 14:58 13.38 13.13 2.33 131.64 14.14 1.22 3.25 0.10 2012/11/03 13:55 14.63 23.34 5.51 114.45 8.60 1.50 4.48 0.15 2012/11/17 11:00 11.90 20.05 2.32 105.59 8.60 1.16 5.23 0.11 2012/12/01 13:23 11.56 0.05 0.62 108.79 24.56 0.44 1.68 0.14 2012/12/15 10:05 6.78 2.69 1.08 176.00 11.63 0.62 3.25 0.06 2012/12/29 09:21 7.76 0.08 0.12 177.00 11.78 0.59 1.69 0.05 2013/01/14 10:53 4.33 0.21 0.14 163.00 14.67 0.81 2.47 0.05 2013/01/26 15:10 8.61 1.30 10.73 0.43 188.00 10.53 0.70 2.47 0.09 2013/02/09 14:42 6.41 0.14 12.42 0.45 166.00 9.46 0.92 5.06 0.06 2013/02/23 12:40 7.92 1.70 11.29 1.74 140.00 7.12 1.62 6.02 0.06 2013/03/10 0.29 2013/04/13 15:00 13.97 3.21 1.97 52.36 9.63 3.67 4.02 0.06 2013/04/27 11:45 14.91 16.70 132.06 1.84 2.90 5.39 0.02 2013/05/11 04:45 14.55 4.90 9.72 4.17 104.36 2.49 3.41 4.96 0.04 2013/05/26 14:45 18.38 25.60 6.79 7.40 32.21 0.50 2.02 3.84 0.00 2013/06/08 12:08 20.21 21.80 6.06 6.33 33.40 0.71 1.57 2.48 0.00 2013/06/22 13:30 21.80 23.10 4.68 6.94 27.60 0.06 1.98 1.95 0.00 2013/07/06 13:50 22.87 26.30 5.64 3.89 44.20 0.31 2.08 2.14 0.00 2013/07/20 13:16 19.31 27.00 4.85 4.75 62.40 1.47 2.09 2.91 0.07 2013/08/16 11:39 23.01 23.36 4.95 4.87 92.80 4.01 1.57 2.39 0.19 2013/08/24 17:10 19.96 26.06 5.62 6.46 64.40 3.30 2.21 4.26 0.16

218

Freshwater Slough (FWS) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/09/07 16:45 20.21 27.92 6.57 7.16 89.60 0.16 1.97 2.66 0.00 2013/09/20 16:45 17.85 25.62 5.98 2.94 100.80 6.96 2.52 3.89 0.15 2013/10/05 14:30 15.17 20.51 9.09 4.59 80.40 7.52 1.46 3.74 0.00 2013/10/19 15:37 13.42 24.66 8.22 1.26 66.40 3.60 1.18 2.55 0.00 2013/11/08 13:50 12.78 28.09 10.07 2.15 47.80 2.64 1.15 3.48 0.00 2013/11/23 18:10 7.94 10.02 10.55 1.14 154.80 5.24 0.96 3.99 0.00 2013/12/07 11:00 4.48 17.66 11.18 0.82 126.60 6.88 0.85 5.43 0.00 2013/12/21 16:00 6.18 19.89 11.32 0.84 99.80 5.42 0.74 4.51 0.00 2014/01/15 13:15 7.72 23.33 10.29 1.95 66.48 5.65 0.75 6.49 0.13 2014/02/02 13:24 8.86 25.61 9.65 3.41 54.35 5.64 0.83 5.85 0.14 2014/02/15 11:39 10.75 0.13 12.01 1.43 93.54 38.58 0.67 2.75 0.29 2014/03/02 18:50 10.95 1.53 10.19 0.29 142.18 13.67 0.65 2.35 0.17 2014/03/15 12:33 13.27 5.34 8.01 1.11 142.77 22.29 0.86 7.27 0.38 2014/03/29 19:54 10.67 0.11 12.12 0.34 98.37 15.24 0.55 1.13 0.31 2014/04/12 10:06 16.07 16.34 7.67 6.67 91.91 0.52 0.48 1.93 0.00 2014/04/26 10:56 15.45 18.56 8.12 6.08 75.53 0.43 0.62 2.21 0.04 2014/05/10 12:55 14.87 5.06 9.23 1.71 93.46 5.74 0.67 1.44 0.11 2014/05/26 12:04 20.40 23.93 6.48 1.54 12.70 0.59 0.75 2.00 0.03 2014/06/14 13:41 20.74 28.75 5.86 1.00 29.60 0.64 1.26 6.82 0.15 2014/06/28 13:29 21.29 28.47 4.62 2.10 63.20 3.07 1.49 6.70 0.35 2014/07/26 10:08 20.28 34.51 6.06 5.00 68.75 2.70 1.40 5.84 0.23 2014/08/05 18:55 21.79 32.17 6.76 5.60 39.85 0.46 1.43 3.91 0.15 2014/08/26 13:23 20.15 33.00 6.32 1.19 12.45 0.25 1.42 4.25 0.09

219

220

Eureka Channel (EC) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/10/13 13:05 13.90 33.30 21.15 5.71 1.86 0.15 2012/10/20 11:38 15.00 32.60 1.20 24.37 5.28 2.27 9.50 0.22 2012/10/27 15:34 13.91 31.44 2.20 25.48 4.41 1.67 10.90 0.26 2012/11/03 12:42 13.60 32.66 1.05 16.45 6.26 1.43 6.58 0.23 2012/11/17 11:49 11.93 32.74 1.73 14.65 5.89 1.24 4.98 0.14 2012/12/01 12:17 13.19 29.34 0.95 20.36 6.20 0.88 5.72 0.16 2012/12/15 10:32 10.88 31.80 2.51 20.01 8.93 1.08 4.95 0.29 2012/12/29 09:45 10.10 28.09 0.89 33.87 11.37 1.00 5.16 1.71 2013/01/14 11:35 8.70 31.01 2.95 29.80 13.22 1.32 4.51 0.18 2013/01/26 14:35 9.90 28.35 9.32 1.24 39.55 11.09 1.27 4.19 0.13 2013/02/09 14:04 9.49 29.49 9.94 6.44 25.63 7.86 1.11 3.18 0.09 2013/02/23 12:10 10.01 29.89 9.55 3.17 29.80 6.47 1.09 3.71 0.11 2013/03/10 2.53 41.71 5.09 1.93 8.86 0.12 2013/04/13 14:30 12.64 31.14 1.72 29.68 6.33 1.91 6.71 0.15 2013/04/27 13:00 12.70 33.20 3.83 25.61 12.43 2.21 6.67 0.16 2013/05/11 10:15 14.98 33.50 9.03 14.68 21.32 0.42 1.03 6.45 0.00 2013/05/26 14:25 12.06 34.10 8.66 6.04 39.71 14.02 2.04 5.51 0.27 2013/06/08 11:15 15.71 33.94 8.81 13.68 10.70 3.31 1.77 3.53 0.04 2013/06/22 14:03 16.83 34.28 9.59 11.70 0.16 1.33 2.11 0.00 2013/07/06 13:25 17.60 34.01 8.92 10.49 6.20 1.43 1.59 2.33 0.02 2013/07/20 12:40 15.22 34.40 8.61 6.38 3.40 1.25 1.75 2.65 0.00 2013/08/16 12:12 21.17 34.52 9.60 3.00 2.00 0.15 1.98 2.31 0.00 2013/08/24 17:35 16.06 34.13 9.54 6.88 14.20 1.62 1.48 2.69 0.00 2013/09/07 16:15 19.41 34.00 8.19 5.87 16.00 0.55 1.91 2.74 0.00

221

Eureka Channel (EC) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/09/20 17:33 17.19 33.52 8.39 3.45 23.60 1.64 2.05 2.63 0.00 2013/10/05 15:00 15.53 32.73 9.25 1.67 25.30 4.96 1.80 4.69 0.10 2013/10/19 16:05 13.03 33.47 9.13 1.61 24.30 6.85 1.68 4.45 0.07 2013/11/08 14:25 10.47 33.78 9.85 1.87 21.90 13.84 1.80 4.68 0.24 2013/11/23 17:40 10.57 32.90 9.94 1.10 18.30 4.77 1.28 5.17 0.09 2013/12/07 10:25 5.95 32.46 10.28 1.03 19.40 3.29 1.12 4.77 0.01 2013/12/21 16:20 7.87 33.09 11.27 1.42 16.10 6.81 1.08 4.31 0.04 2014/01/15 13:45 9.78 32.93 10.52 1.25 14.19 6.51 1.13 4.99 0.18 2014/02/02 12:58 9.95 33.44 8.83 0.90 16.29 11.87 1.36 4.01 0.24 2014/02/15 11:58 11.19 31.67 1.38 14.77 7.69 1.03 4.91 0.22 2014/03/02 18:08 13.31 27.37 9.16 2.01 33.69 5.71 0.87 4.63 0.25 2014/03/15 12:03 11.91 31.15 8.71 0.68 21.66 9.40 1.18 5.77 0.34 2014/03/29 11:40 10.79 32.61 9.56 1.09 14.86 8.03 0.99 4.68 0.15 2014/04/12 10:35 12.59 32.07 8.78 1.51 19.41 9.29 1.24 5.94 0.26 2014/04/26 11:15 11.48 33.19 9.04 2.20 16.96 12.10 1.33 4.38 0.22 2014/05/10 13:14 17.58 32.30 7.64 1.32 23.57 1.53 1.33 5.79 0.15 2014/05/26 12:26 14.96 33.74 8.28 3.68 24.39 5.45 1.36 5.59 0.24 2014/06/14 14:07 12.82 34.30 7.72 4.60 34.95 14.07 1.67 5.85 0.39 2014/06/28 14:20 15.96 34.26 9.53 4.40 18.08 1.39 1.09 7.33 0.19 2014/07/26 10:25 18.74 34.55 6.95 2.00 36.10 1.75 2.02 9.26 0.22 2014/08/05 19:21 13.96 34.06 9.27 5.60 19.70 6.71 1.31 7.41 0.35 2014/08/26 12:58 15.90 34.14 8.14 3.33 16.31 2.05 1.47 9.11 0.27 2014/09/02 13:57 19.60 34.52 7.12 4.60 35.84 1.43 2.16 7.44 0.30 2014/09/16 13:51 17.30 34.34 9.19 2.60 31.47 3.36 1.88 7.50 0.30

222

Jacoby Creek (JC) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/09/25 16:15 14.85 10.09 58.50 86.40 1.23 1.42 0.30 2014/10/24 19:51 13.99 0.08 10.60 0.24 51.70 94.00 0.93 1.75 0.18 2014/11/29 15:21 11.70 0.06 1.24 35.40 59.90 0.90 3.22 0.27 2014/12/12 1.77 36.00 68.80 0.70 1.61 0.17

Elk River (ER) station water quality data (Hurst, 2015 b.). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2014/09/25 17:15 17.70 22.45 25.30 43.30 3.51 14.53 1.34 2014/10/24 18:25 15.30 19.34 6.00 0.77 24.10 34.10 2.16 11.02 0.71 2014/11/29 13:59 12.87 23.54 0.87 18.80 18.60 1.74 9.37 0.45

223

Bay Entrance (BE) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Silicate Nitrate Phosphate Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µM) (µM) (µM) (µM) 2007/10/12 11.10 33.27 8.82 18.29 18.06 1.12 0.29 2007/10/17 12.94 33.34 9.25 5.87 5.66 0.77 0.21 2007/10/26 10.00 33.91 7.97 27.81 18.48 1.55 0.38 2007/11/09 10.52 33.17 8.35 16.04 12.85 1.25 0.19 2007/11/21 10.19 33.28 6.89 19.95 13.24 1.31 0.24 2007/12/07 10.48 32.29 9.51 18.34 11.50 1.11 0.25 2007/12/13 8.96 33.60 7.01 26.86 17.45 1.27 0.26 2007/12/28 8.98 32.73 9.37 14.42 9.90 0.90 0.17 2008/01/11 10.06 30.35 9.42 16.76 6.94 0.84 0.25 2008/01/25 9.15 31.88 9.26 21.85 13.79 1.43 0.18 2008/02/08 9.34 32.80 8.92 21.35 15.15 1.34 0.35 2008/02/26 9.39 32.83 8.64 18.21 12.67 1.19 0.20 2008/03/07 9.22 33.25 7.75 25.14 17.62 1.39 0.28 2008/03/21 9.06 33.16 7.86 6.51 9.77 1.94 0.16 2008/04/04 8.65 33.51 6.68 9.52 39.71 7.85 0.22 2008/04/18 8.56 33.00 6.94 13.64 8.04 0.81 0.43 2008/05/02 8.52 33.70 5.70 11.03 12.07 0.90 0.27 2008/05/16 8.25 33.83 7.03 9.64 17.82 1.37 0.37 2008/05/23 8.55 33.90 8.55 14.46 13.86 1.18 0.26 2008/06/06 10.51 33.66 10.11 5.44 13.38 0.96 0.13 2008/06/20 8.34 33.97 5.25 24.16 16.91 1.17 0.50 2008/07/03 9.96 33.52 8.52 7.46 2.21 0.42 0.35 2008/07/18 10.95 33.93 8.68 9.63 24.34 2.14 0.31 2008/08/01 11.07 33.83 9.30 5.73 9.33 0.79 0.27

224

Bay Entrance (BE) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µM) (µM) (µM) (µM) (µM) 2008/08/15 9.58 33.66 6.76 14.79 11.03 0.96 0.40 2008/08/29 10.78 33.82 7.99 9.09 8.33 0.84 0.27 2008/09/12 10.88 33.97 9.25 12.90 18.37 1.65 0.29 2008/09/26 11.81 33.58 7.91 7.47 10.89 1.41 0.54 2008/10/10 10.08 33.57 7.59 9.26 16.45 1.44 0.31 2008/10/30 10.17 33.53 8.76 23.41 12.46 1.39 2008/11/14 11.24 33.07 8.48 16.26 7.39 1.02 2008/12/24 9.19 31.96 9.55 16.89 7.42 0.88 2009/01/09 9.52 32.68 8.41 17.40 9.00 1.05 2009/01/23 9.80 32.76 8.94 16.76 8.39 0.66 2009/01/30 9.06 33.59 7.41 21.99 13.50 1.20 2009/02/13 9.05 32.40 9.55 14.02 9.70 0.72 2009/02/27 10.14 30.49 9.19 15.53 5.77 0.71 2009/03/13 9.41 32.71 7.88 15.91 9.77 0.88 2009/03/27 8.34 32.59 4.99 30.29 17.84 2.17 2009/04/10 8.88 33.29 9.12 16.48 13.07 1.25 2009/04/24 8.05 32.24 6.28 36.56 20.31 2.56 2009/05/08 10.21 32.87 8.79 16.65 12.11 1.29 2009/05/22 8.76 33.61 7.83 43.36 17.50 1.82 2009/06/05 10.31 33.45 5.66 3.91 0.58 2009/06/14 10.84 33.04 9.01 6.97 3.97 0.75 2009/07/02 10.53 31.19 10.51 15.56 2.25 0.62 2012/10/04 14:06 10.24 33.66 8.03 19.29 15.88 1.56 5.00 0.23 2012/10/18 13:24 11.39 33.28 9.34 7.60 5.87 0.87 3.58 0.13

225

Bay Entrance (BE) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/11/02 13:02 11.99 33.14 8.92 9.09 7.31 0.86 2.40 0.14 2012/11/16 12:02 11.97 33.08 9.07 1.80 11.66 4.68 0.72 2.48 0.08 2012/12/04 13:44 13.30 30.41 8.72 0.33 18.90 3.93 0.72 3.74 0.12 2012/12/14 11:10 11.42 32.77 8.17 0.23 13.42 8.83 0.99 2.59 0.24 2012/12/28 10:33 10.73 29.15 9.25 0.51 26.02 6.21 0.81 2.51 0.29 2013/01/11 09:55 10.10 33.08 8.35 0.80 18.70 13.08 1.26 2.06 0.10 2013/01/25 09:07 9.54 32.28 9.19 1.06 24.26 15.96 1.39 2.18 0.07 2013/02/08 08:36 9.29 32.51 10.08 6.26 15.14 11.71 1.02 2.10 0.13 2013/02/21 07:55 8.28 33.73 8.13 2.09 36.96 26.41 2.15 2.80 0.16 2013/03/12 12:28 8.78 33.74 8.29 1.97 27.95 23.85 2.04 4.27 0.13 2013/03/29 13:45 9.45 32.80 10.27 7.15 7.94 7.69 0.79 4.28 0.11 2013/04/12 13:22 8.47 33.79 5.94 1.88 34.97 24.65 2.42 6.02 0.16 2013/04/26 12:39 9.19 33.78 8.34 2.26 34.37 25.08 2.22 3.67 0.19 2013/05/10 13:06 9.30 33.44 8.38 8.54 28.45 17.14 1.73 3.55 0.06 2013/05/24 12:06 9.24 33.76 8.17 5.11 32.28 22.98 2.11 4.59 0.33 2013/06/07 12:26 9.76 33.08 8.21 9.77 16.60 11.07 1.56 2.43 0.13 2013/06/21 10:50 9.43 33.89 6.04 8.82 29.70 20.47 2.06 4.18 0.23 2013/07/02 08:20 11.36 33.75 7.26 5.99 20.20 11.93 1.45 4.61 0.23 2013/07/19 09:18 11.11 33.80 9.72 9.39 4.30 6.37 0.88 2.76 0.00 2013/08/15 07:17 10.36 33.62 6.67 4.52 19.30 15.66 2.11 7.00 0.18 2013/08/23 13:30 10.58 33.36 8.60 5.66 15.70 12.36 1.33 1.67 0.03 2013/09/06 13:00 12.27 33.23 9.27 6.78 8.60 6.15 1.01 3.04 0.15 2013/09/18 11:13 10.71 34.13 6.92 6.59 22.80 13.85 1.71 2.62 0.00 2013/10/04 11:19 9.96 33.86 7.53 0.07 23.30 16.17 1.71 1.89 0.12

226

Bay Entrance (BE) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/10/18 11:01 9.41 31.86 6.53 2.54 28.30 20.52 1.99 2.78 0.13 2013/11/07 12:50 9.55 31.75 8.01 1.80 23.10 18.59 1.86 2.70 0.23 2013/11/22 13:14 9.79 31.74 8.47 1.22 17.90 14.21 1.58 2.83 0.13 2013/12/06 13:20 8.94 33.13 7.73 0.54 20.30 15.70 1.57 1.92 0.01 2013/12/20 12:26 8.69 33.68 6.75 0.77 24.30 19.46 1.80 1.86 0.00 2014/01/14 09:07 9.92 33.29 9.71 2.36 14.75 12.57 1.35 3.03 0.23 2014/01/31 10:38 9.92 33.29 9.11 1.07 14.21 12.77 1.30 1.51 0.24 2014/02/14 10:31 11.02 31.60 9.28 0.77 14.28 7.22 0.90 1.40 0.16 2014/02/28 09:50 11.08 32.68 9.27 1.73 9.28 4.97 0.70 1.53 0.11 2014/03/14 10:19 11.05 32.69 8.56 0.41 14.63 9.33 1.05 2.10 0.27 2014/03/28 08:38 10.27 33.06 9.72 1.73 15.75 10.01 0.98 1.62 0.11 2014/04/11 09:51 10.19 33.62 8.15 1.59 18.98 16.03 1.46 2.96 0.24 2014/04/25 08:51 9.72 33.65 8.58 3.17 23.48 20.60 1.64 1.82 0.14 2014/05/09 08:27 10.87 33.25 9.04 3.52 17.33 12.84 1.22 3.19 0.21 2014/05/23 07:45 9.26 33.81 5.57 2.10 24.93 20.62 1.81 3.59 0.32 2014/06/13 13:09 9.80 34.08 7.95 4.57 32.34 19.78 1.35 3.94 0.48 2014/06/27 13:06 11.83 33.81 13.03 9.78 0.01 0.06 0.02 4.05 0.00 2014/07/11 5.69 12.16 10.67 0.96 3.75 0.24 2014/07/25 11:38 11.56 33.95 7.81 2.54 18.53 13.56 1.40 5.44 0.30 2014/08/08 10:53 11.50 33.55 9.88 10.16 5.06 6.64 0.66 3.47 0.17 2014/08/22 10:55 12.61 34.36 9.69 5.85 4.39 5.54 0.65 3.21 0.12 2014/09/04 08:45 11.87 34.40 8.70 1.34 15.09 9.69 1.50 5.70 0.37 2014/09/19 09:40 14.15 34.27 9.92 2.66 11.65 2.02 0.39 2.16 0.00 2014/10/03 08:22 12.42 34.30 7.11 1.39 18.03 10.03 1.37 2.63 0.29

227

228

Indian Island (II) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Silicate Nitrate Phosphate Nitrite Date/Time (LST) (µM) (µM) (µM) (µM) 2007/10/12 20.34 15.31 1.69 0.31 2007/10/17 17.22 5.75 1.45 0.32 2007/10/26 18.01 9.68 1.49 0.38 2007/11/09 20.40 8.41 1.47 0.32 2007/11/21 15.02 7.85 1.26 0.31 2007/12/07 23.92 13.73 1.16 0.29 2007/12/13 28.68 18.61 1.60 0.35 2007/12/28 32.06 19.38 1.57 0.33 2008/01/11 34.93 8.52 0.78 0.30 2008/01/25 28.11 17.48 1.59 0.24 2008/02/08 34.96 9.97 0.94 0.39 2008/02/26 38.08 15.33 1.47 0.26 2008/03/07 25.73 20.79 1.85 0.30 2008/03/21 6.54 10.79 1.09 0.25 2008/04/04 8.19 13.69 1.24 0.26 2008/04/18 6.16 5.31 0.67 0.12 2008/05/02 5.99 6.84 0.91 0.07 2008/05/16 5.65 0.37 0.58 0.16 2008/05/23 7.30 0.03 0.51 0.27 2008/06/06 5.80 0.55 0.45 0.17 2008/06/20 20.46 2.86 0.60 0.43 2008/07/03 8.22 0.86 0.60 0.30 2008/07/18 9.67 14.90 1.85 0.35 2008/08/01 6.20 6.02 1.21 0.28

229

Indian Island (II) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µM) (µM) (µM) (µM) (µM) 2008/08/15 11.33 5.50 1.41 0.39 2008/08/29 10.51 3.76 1.05 0.27 2008/09/12 19.37 6.56 2.00 0.38 2008/09/26 9.06 7.99 1.65 0.36 2008/10/10 9.29 11.36 2.26 0.29 2008/10/30 18.21 6.09 1.28 2008/11/14 21.51 6.30 1.46 2008/12/24 21.44 8.08 1.35 2009/01/09 22.37 9.39 1.10 2009/01/23 17.28 8.32 1.03 2009/01/30 11.16 4.71 0.73 2009/02/13 21.30 7.33 1.00 2009/02/27 31.86 5.89 1.05 2009/03/13 23.21 5.81 1.05 2009/03/27 19.06 7.15 0.94 2009/04/10 3.85 1.48 0.94 2009/04/24 25.06 2.88 1.35 2009/05/08 15.16 2.27 1.09 2009/05/22 22.55 2.08 1.33 2009/06/05 14.79 0.48 2.57 2009/06/14 19.60 0.16 1.52 2009/07/02 16.42 1.06 1.54 2012/10/04 14:46 14.24 33.78 8.59 25.74 10.52 1.85 8.78 0.22 2012/10/18 14:11 14.66 33.17 8.80 17.83 5.11 1.51 7.14 0.25

230

Indian Island (II) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/11/02 13:53 14.05 32.67 8.81 18.56 3.78 1.49 7.26 0.24 2012/11/16 13:03 12.09 32.79 9.05 1.38 15.37 4.50 1.25 4.93 0.20 2012/12/04 13:04 12.68 24.59 8.76 1.60 47.47 11.28 1.44 10.38 0.39 2012/12/14 12:15 11.33 31.58 8.71 0.61 20.32 7.73 1.13 5.85 0.30 2012/12/28 11:57 9.68 25.06 9.06 0.51 47.61 10.31 1.14 7.24 0.34 2013/01/11 11:21 9.80 31.42 9.24 0.40 26.03 10.99 1.27 4.73 0.24 2013/01/25 10:22 9.32 31.30 9.25 1.86 29.61 12.23 1.42 5.35 0.17 2013/02/08 09:33 9.12 32.21 9.54 3.66 19.74 12.39 1.29 4.25 0.18 2013/02/21 09:06 8.81 31.57 9.25 1.69 32.11 9.35 1.34 5.06 0.12 2013/03/12 13:21 10.62 31.62 9.76 1.15 25.34 14.40 1.69 4.99 0.16 2013/03/29 14:50 12.80 31.97 10.36 1.53 17.36 6.97 1.33 5.02 0.11 2013/04/12 14:17 12.29 31.35 8.54 1.01 22.47 10.16 1.82 8.50 0.17 2013/04/26 13:54 12.51 32.86 8.87 3.04 31.96 14.25 2.04 5.06 0.17 2013/05/10 13:41 13.74 33.04 9.36 6.64 31.64 8.20 1.61 4.81 0.14 2013/05/24 13:06 13.91 33.40 8.89 5.01 26.20 9.69 1.92 5.14 0.20 2013/06/07 13:03 15.73 33.02 9.28 8.74 11.50 4.33 1.54 2.49 0.09 2013/06/21 11:50 16.76 34.18 9.48 16.75 5.40 0.83 1.64 2.05 0.00 2013/07/02 09:11 19.26 33.89 7.44 5.65 6.80 0.49 1.97 3.05 0.00 2013/07/19 10:27 16.86 34.35 8.02 4.40 4.40 0.05 2.12 1.96 0.00 2013/08/15 09:03 18.57 33.83 8.45 4.10 3.30 0.02 2.00 2.22 0.00 2013/08/23 14:16 13.32 33.57 9.48 8.74 12.70 3.76 1.22 2.88 0.00 2013/09/06 14:04 17.31 33.38 9.01 7.48 6.80 0.25 1.22 1.86 0.00 2013/09/18 12:29 16.48 34.26 8.62 2.18 17.20 2.66 1.77 1.95 0.00 2013/10/04 12:15 14.34 33.05 8.07 1.22 20.20 5.72 1.49 3.45 0.12

231

Indian Island (II) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/10/18 12:18 11.92 31.59 8.96 0.81 25.70 9.93 1.69 2.71 0.09 2013/11/07 14:01 11.39 31.66 9.89 0.95 20.60 11.01 1.64 2.81 0.17 2013/11/22 14:24 11.37 31.35 10.63 0.94 16.30 4.17 1.24 3.56 0.04 2013/12/06 14:11 8.60 32.71 9.64 0.79 17.30 6.89 1.33 3.56 0.04 2013/12/20 13:33 7.19 32.82 9.13 1.37 15.70 7.86 1.19 3.00 0.02 2014/01/14 10:04 9.01 32.92 8.82 0.64 13.68 6.90 1.08 4.61 0.19 2014/01/31 11:54 10.63 33.06 9.45 1.05 14.58 8.54 1.15 3.63 0.19 2014/02/14 11:15 11.52 21.25 8.10 0.73 2014/02/28 11:01 11.67 31.42 8.98 1.14 17.68 7.53 1.03 4.18 0.25 2014/03/14 11:32 12.74 29.35 8.15 1.32 27.67 8.77 1.17 7.49 0.36 2014/03/28 09:44 11.69 31.56 8.10 0.98 27.27 11.04 1.31 4.46 0.24 2014/04/11 10:47 13.07 31.69 8.41 0.87 20.90 8.28 1.26 5.95 0.25 2014/04/25 09:58 12.88 32.61 8.05 2.00 17.91 8.66 1.37 4.84 0.29 2014/05/09 09:23 15.10 33.12 7.30 1.20 16.28 3.45 1.46 7.69 0.21 2014/05/23 09:07 16.01 33.46 6.94 0.96 21.04 3.40 1.35 5.07 0.18 2014/06/13 14:11 13.64 34.32 7.50 1.43 33.71 14.01 1.76 6.53 0.56 2014/06/27 14:28 15.28 34.50 9.10 7.77 17.76 2.33 1.09 5.61 0.23 2014/07/11 13:13 16.75 34.81 8.16 3.84 20.88 1.93 1.08 6.98 0.20 2014/07/25 12:35 16.70 34.30 8.04 5.11 21.17 2.45 1.25 5.96 0.21 2014/08/08 11:56 16.79 34.57 7.96 6.04 27.50 3.85 1.60 6.94 0.31 2014/08/22 11:42 16.49 34.72 7.03 1.22 23.73 8.58 1.86 8.32 0.31 2014/09/04 09:12 17.65 35.02 7.06 1.64 35.88 2.50 2.09 5.47 0.24 2014/09/19 11:32 17.32 34.61 7.33 0.74 27.96 2.79 1.73 8.74 0.27 2014/10/03 09:31 16.67 33.66 6.92 1.88 34.34 4.74 2.23 8.29 0.47

232

233

Mad River Slough (MRS) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Silicate Nitrate Phosphate Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µM) (µM) (µM) (µM) 2007/10/12 14.66 33.35 7.58 18.76 1.44 1.29 0.24 2007/10/17 13.70 32.90 7.67 20.88 2.70 2.07 0.25 2007/10/26 13.77 31.03 8.14 22.60 4.06 1.87 0.41 2007/11/09 12.59 32.22 8.47 19.97 5.41 1.70 0.33 2007/11/21 11.03 31.16 7.99 21.04 5.92 1.74 0.42 2007/12/07 10.32 30.21 8.71 26.15 9.02 1.01 0.36 2007/12/13 7.99 29.63 9.17 36.56 16.21 1.35 0.41 2007/12/28 7.09 27.36 9.55 50.03 20.90 1.63 0.41 2008/01/11 9.04 21.45 9.58 66.29 18.83 1.52 0.48 2008/01/25 7.39 28.91 9.77 41.06 16.95 1.39 0.27 2008/02/08 9.68 24.13 9.77 52.09 16.20 1.38 0.36 2008/02/26 10.81 28.79 9.20 39.07 14.69 1.52 0.29 2008/03/07 10.95 29.14 9.34 28.34 9.31 1.08 0.20 2008/03/21 12.23 27.34 9.91 13.63 5.71 1.85 0.24 2008/04/04 12.23 30.05 8.90 6.96 2.83 2.01 0.11 2008/04/18 13.36 32.08 7.83 8.95 4.75 1.27 0.07 2008/05/02 14.05 31.79 8.18 8.37 1.00 1.03 0.06 2008/05/16 17.96 33.32 8.73 6.60 0.45 1.27 0.08 2008/05/23 13.33 33.68 7.68 13.57 0.15 1.18 0.24 2008/06/06 15.39 33.84 7.98 9.11 0.00 0.87 0.14 2008/06/20 17.55 34.25 8.64 15.32 3.43 1.76 0.15 2008/07/03 18.23 34.30 8.73 11.55 0.91 1.59 0.16 2008/07/18 17.42 33.69 7.34 9.12 2.60 1.85 0.10 2008/08/01 19.34 34.22 8.83 5.61 0.99 1.88 0.08

234

Mad River Slough (MRS) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µM) (µM) (µM) (µM) (µM) 2008/08/15 18.84 34.28 7.89 8.64 2.55 2.50 0.14 2008/08/29 18.71 34.00 7.38 17.28 0.18 1.79 0.22 2008/09/12 16.61 34.35 8.26 16.78 0.73 2.26 0.22 2008/09/26 16.44 33.95 8.22 13.46 1.97 2.61 0.20 2008/10/06 17.21 33.46 7.48 14.97 1.96 2.88 0.21 2008/10/30 13.02 33.62 8.90 10.85 1.66 1.36 2008/11/14 13.71 31.52 8.22 15.95 3.30 1.08 2008/12/24 7.17 29.96 9.66 21.71 6.57 2.27 2009/01/09 8.95 27.38 8.82 27.64 11.04 1.36 2009/01/23 9.75 29.93 9.39 13.23 7.06 0.79 2009/01/30 9.47 30.78 9.91 12.67 3.71 0.85 2009/02/13 6.82 28.47 9.74 16.66 5.14 1.07 2009/02/27 11.81 24.97 8.08 32.67 6.99 1.15 2009/03/13 11.92 27.14 8.42 2009/03/27 13.30 26.58 9.60 13.34 2.13 0.85 2009/04/10 12.66 29.92 9.21 2.82 0.37 0.83 2009/04/24 15.44 31.82 7.56 19.41 1.34 1.30 2009/05/08 16.45 27.66 7.40 13.15 1.35 1.85 2009/05/22 16.54 31.87 7.61 17.82 0.78 2009/06/05 15.75 33.15 25.68 0.41 1.68 2009/06/14 18.66 33.49 7.89 25.85 0.06 2.15 2009/07/02 18.26 31.41 8.55 18.85 0.03 1.75 2012/10/04 08:24 16.92 33.83 7.61 24.57 1.08 2.14 6.39 0.03 2012/10/18 09:02 15.48 33.11 7.43 31.35 4.68 2.75 6.71 0.18

235

Mad River Slough (MRS) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/11/02 15:05 14.72 32.38 8.11 25.98 4.49 1.86 6.84 0.20 2012/11/16 14:32 12.32 32.25 8.65 1.84 24.16 4.89 1.84 5.49 0.25 2012/12/04 14:13 12.07 19.97 9.20 3.83 68.03 25.17 2.53 16.31 0.71 2012/12/14 15:56 10.10 25.63 8.58 1.64 42.46 9.70 1.70 10.20 0.42 2012/12/28 12:44 8.76 22.67 8.94 1.31 58.84 27.01 1.64 11.16 1.83 2013/01/11 12:30 8.57 27.92 9.15 1.62 43.29 11.52 1.52 6.94 0.31 2013/01/25 11:22 9.41 29.71 9.40 3.34 35.01 9.31 1.37 4.82 0.14 2013/02/08 10:52 9.21 30.11 9.35 2.28 21.89 4.57 1.17 4.59 0.06 2013/02/21 10:19 9.14 30.82 10.05 3.23 17.40 1.30 0.90 3.76 0.06 2013/03/12 14:29 11.86 29.43 9.91 2.75 19.75 4.49 1.31 4.38 0.04 2013/03/29 15:56 14.95 31.17 9.90 2.35 18.18 1.82 1.32 4.99 0.01 2013/04/12 15:34 14.62 30.09 8.55 2.63 28.47 2.65 1.75 6.48 0.09 2013/04/26 14:43 15.00 32.57 9.17 2.41 27.18 3.18 1.81 5.78 0.04 2013/05/10 15:06 15.92 33.34 9.97 10.02 16.98 0.00 1.29 4.96 0.00 2013/05/24 14:15 16.94 34.02 8.74 4.67 20.29 0.60 1.85 4.69 0.00 2013/06/07 14:09 17.63 33.08 9.54 9.49 4.50 0.12 1.79 8.13 0.00 2013/06/21 12:40 19.08 34.37 8.49 11.10 2.70 0.11 2.27 2.46 0.00 2013/07/02 10:39 20.94 34.19 7.01 6.82 5.60 0.02 2.84 2.23 0.00 2013/07/19 11:33 17.91 34.52 7.73 4.62 0.90 0.06 2.83 2.31 0.00 2013/08/15 10:14 20.34 34.02 7.96 3.63 2.00 0.05 2.75 2.19 0.00 2013/08/23 15:38 17.87 34.06 7.66 3.56 22.50 1.24 2.44 4.52 0.00 2013/09/06 15:07 21.36 33.94 7.54 3.75 22.80 0.17 3.03 2.22 0.00 2013/09/18 13:16 18.61 34.48 7.84 2.04 21.50 0.25 2.43 2.31 0.00 2013/10/04 14:43 16.00 32.46 7.39 1.35 24.70 0.82 2.21 3.30 0.00

236

Mad River Slough (MRS) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/10/18 13:45 13.51 31.26 8.74 0.44 20.90 3.12 1.74 3.21 0.00 2013/11/07 15:16 12.36 31.55 9.62 0.63 15.40 2.23 1.29 2.84 0.00 2013/11/22 15:10 10.78 31.33 9.62 1.08 17.80 3.69 1.23 4.02 0.08 2013/12/06 15:12 7.51 32.50 9.71 1.54 17.00 2.41 1.22 4.20 0.02 2013/12/20 16:24 6.90 32.95 9.86 0.87 13.90 3.46 1.04 3.73 0.00 2014/01/14 11:30 8.87 32.42 8.76 0.86 14.81 3.30 1.02 5.08 0.14 2014/01/31 12:46 10.44 32.62 9.00 1.05 14.55 3.95 1.05 4.32 0.15 2014/02/14 13:40 12.09 29.92 7.75 1.11 23.33 5.12 1.28 10.80 0.31 2014/02/28 11:48 12.21 29.76 8.38 0.96 21.29 5.28 1.04 5.50 0.30 2014/03/14 12:55 13.61 26.51 7.89 1.44 34.73 7.36 1.47 10.32 0.47 2014/03/27 13:51 13.67 29.02 8.10 1.27 27.87 5.04 1.53 5.47 0.22 2014/04/11 11:54 14.82 29.90 8.24 1.15 22.85 2.96 1.25 5.24 0.18 2014/04/25 10:52 14.29 31.82 7.79 0.06 17.66 2.41 1.40 5.00 0.16 2014/05/09 10:35 16.37 32.94 6.77 0.28 21.92 1.50 1.71 5.30 0.13 2014/05/23 10:14 18.21 33.56 6.17 0.52 30.32 1.51 1.77 5.13 0.15 2014/06/13 15:15 18.71 34.59 7.50 1.03 42.57 3.22 1.95 6.84 0.22 2014/06/27 15:25 19.46 34.87 6.34 2.00 42.23 2.09 2.17 8.61 0.28 2014/07/11 14:17 19.31 35.29 6.47 2.61 51.01 1.98 2.42 7.73 0.28 2014/07/25 13:57 20.06 34.77 6.58 3.27 42.21 1.43 2.07 6.35 0.24 2014/08/08 13:04 19.68 35.04 6.73 3.35 53.74 2.56 2.51 7.06 0.31 2014/08/22 13:16 2.03 35.13 6.69 0.61 42.09 2.07 2.35 5.68 0.34 2014/09/04 22:47 18.51 35.31 6.72 0.40 44.08 2.34 2.55 6.10 0.32 2014/09/19 12:16 19.08 34.87 6.36 0.92 42.76 3.02 2.39 7.75 0.36 2014/10/03 10:46 18.15 33.57 7.05 1.66 41.13 4.90 2.60 7.87 0.54

237

238

Hookton Slough (HS) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µM) (µM) (µM) (µM) (µM) 2012/10/04 09:08 14.67 33.17 7.32 20.86 1.75 1.45 9.34 0.11 2012/10/18 14:45 15.32 32.46 8.08 22.00 3.98 1.63 7.16 0.17 2012/11/01 15:20 14.64 32.18 8.63 21.23 5.71 1.43 6.70 0.20 2012/11/15 14:44 11.83 32.00 8.90 30.99 6.64 1.53 7.95 0.30 2012/12/04 09:05 11.74 20.47 8.83 68.46 19.28 1.20 9.32 0.38 2012/12/13 12:33 9.43 27.91 8.56 53.98 11.66 1.21 9.64 0.39 2013/01/10 14:17 8.72 12.29 10.28 110.19 20.43 0.92 5.09 0.21 2013/01/24 13:55 10.03 21.16 9.53 76.73 14.10 0.87 5.97 0.17 2013/02/07 14:10 9.25 13.77 11.12 109.81 15.09 0.79 4.50 0.10 2013/02/20 12:08 9.82 19.95 10.69 73.92 7.77 0.50 2.45 0.05 2013/03/11 15:11 11.89 25.77 10.82 50.55 7.00 1.99 7.73 0.05 2013/03/28 15:22 13.18 31.00 10.07 20.27 3.47 1.39 6.51 0.02 2013/04/11 15:16 14.05 23.05 10.11 55.90 4.08 2.22 8.60 0.06 2013/04/25 14:42 15.44 31.49 10.60 22.86 2.93 1.65 4.86 0.04 2013/05/09 15:04 15.55 31.45 9.77 21.84 0.92 1.35 6.96 0.05 2013/05/23 15:19 19.57 31.53 9.69 23.34 0.00 1.95 4.62 0.00 2013/06/06 14:00 17.63 31.50 9.96 4.00 1.86 1.39 1.14 2.11 2013/06/20 13:37 21.76 32.66 10.31 6.20 0.41 1.75 1.23 2.11 2013/07/02 11:28 20.78 33.48 6.41 1.50 0.02 1.41 1.38 2.11 2013/07/19 12:21 17.85 34.00 6.18 7.10 0.18 1.68 1.83 0.00 2013/08/15 11:06 21.68 33.39 7.51 22.30 0.05 1.47 1.12 2.11 2013/08/23 15:39 17.77 33.84 7.17 20.00 1.60 1.57 3.55 0.06 2013/09/05 15:11 22.16 33.82 6.41 26.30 0.83 1.94 1.86 0.02 2013/09/17 14:53 20.39 34.05 8.52 33.70 1.29 1.75 2.17 0.09

239

Hookton Slough (HS) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/10/03 14:30 16.89 28.73 8.96 46.20 3.03 1.35 4.73 0.21 2013/10/17 14:55 13.78 31.14 9.30 27.30 2.73 1.23 3.58 0.06 2013/11/06 14:23 12.10 31.42 8.59 26.30 5.13 1.17 8.12 0.31 2013/11/21 15:38 11.97 29.72 9.04 31.70 6.11 1.03 7.67 0.37 2013/12/05 15:20 7.02 32.23 9.30 28.40 5.17 0.87 9.00 0.35 2013/12/19 15:36 7.13 32.54 9.81 36.00 8.59 0.81 9.06 0.40 2014/03/27 09:49 11.36 31.84 8.05 0.99 31.40 13.24 1.40 5.88 0.25 2014/04/09 12:09 15.54 22.36 7.15 2.03 68.68 8.72 0.68 7.73 0.38 2014/04/25 12:57 14.38 26.26 8.11 2.40 43.04 5.66 0.44 6.34 0.25 2014/05/07 11:48 16.14 27.79 7.42 4.67 37.34 0.40 0.36 1.98 0.00 2014/05/22 10:58 18.83 31.98 7.06 1.77 21.28 0.36 0.62 2.21 0.00 2014/06/12 15:03 19.62 34.55 7.97 1.66 37.34 1.71 1.65 8.04 0.25 2014/06/26 15:00 18.93 34.42 7.17 4.27 28.59 2.03 1.09 4.61 0.27 2014/07/10 13:32 18.75 34.90 7.04 3.24 40.43 1.79 1.91 5.36 0.23 2014/07/24 14:12 20.87 34.39 7.66 3.22 37.70 0.93 1.91 3.23 0.21 2014/08/07 14:10 19.33 34.65 7.73 5.76 44.60 2.53 1.71 4.82 0.33 2014/08/21 14:27 21.49 34.88 8.50 1.68 34.66 0.50 1.51 2.67 0.12 2014/09/02 11:24 20.21 35.34 5.93 1.63 43.43 0.92 1.40 2.46 0.03 2014/09/18 01:23 19.51 34.20 6.12 1.26 36.73 6.82 1.32 6.76 0.48 2014/10/01 11:41 17.63 32.70 6.10 1.82 41.36 11.30 1.44 9.89 0.69 2014/10/22 15:00 15.65 32.47 7.32 1.93 37.76 9.19 1.49 9.36 0.63 2014/11/05 14:28 15.49 29.69 7.70 3.02 43.54 10.00 1.25 10.58 0.54 2014/11/18 10:08 11.96 33.00 7.36 0.33 36.54 12.20 1.71 7.64 0.56 2014/12/04 02:37 14.18 20.12 8.38 1.42 104.87 28.05 1.06 7.92 0.59

240

241

Samoa Channel (SC) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2012/12/04 12.78 25.26 8.80 1.11 48.16 9.55 1.27 8.21 0.25 2012/12/14 11.42 32.65 8.28 0.51 10.58 6.42 0.81 4.17 0.17 2012/12/28 10.51 28.93 8.88 0.82 29.08 7.73 0.97 5.12 0.31 2013/01/11 10.07 32.72 8.54 0.89 19.99 11.60 1.25 3.41 0.14 2013/01/25 9.53 32.62 9.25 1.89 23.79 14.68 1.41 3.94 0.11 2013/02/08 9.31 32.69 10.01 6.44 14.23 10.85 1.02 3.36 0.15 2013/02/21 8.78 32.96 9.66 1.12 31.12 19.90 1.84 4.03 0.15 2013/03/12 9.35 33.21 8.86 6.30 21.31 19.26 1.91 4.58 0.14 2013/03/29 9.90 32.77 9.96 5.20 7.46 8.62 1.03 4.67 0.12 2013/04/12 11.01 32.48 8.10 7.60 27.12 13.78 1.93 7.06 0.18 2013/04/26 10.30 33.45 8.64 27.23 19.24 2.10 4.31 0.17 2013/05/10 10.87 33.95 8.35 5.70 28.50 14.92 1.85 5.23 0.12 2013/05/24 10.27 34.16 8.82 6.22 30.38 18.78 2.00 5.55 0.30 2013/06/07 12.07 33.02 8.30 10.57 25.00 15.04 1.97 3.38 0.25 2013/06/21 13.25 33.91 9.33 10.20 5.01 1.40 2.30 0.02 2013/07/02 17.68 33.76 7.96 7.94 6.40 1.39 1.61 3.85 0.00 2013/07/19 14.34 34.03 8.98 7.69 2.40 1.80 1.46 2.34 0.00 2013/08/15 16.06 33.64 9.20 4.81 3.30 0.65 1.29 2.30 0.00 2013/08/23 11.37 33.40 9.26 7.90 12.80 7.82 1.05 2.57 0.03 2013/09/06 14.00 33.23 9.68 6.31 6.90 2.78 0.77 1.85 0.00 2013/09/18 11.33 34.12 7.34 1.24 20.60 12.03 1.47 3.23 0.14 2013/10/04 11.75 33.57 7.96 1.02 23.20 12.71 1.62 2.75 0.14 2013/10/18 9.89 31.79 7.64 3.02 27.10 18.20 1.81 2.18 0.13 2013/11/07 9.77 31.78 8.53 1.39 24.10 18.46 1.86 2.88 0.26

242

Samoa Channel (SC) station water quality data (Wiyot Tribe Natural Resources Department, 2015). Temp. Salinity DO Chl-A Silicate Nitrate Phosphate Ammonium Nitrite Date/Time (LST) (°C) (ppt) (mg/L) (µg/L) (µM) (µM) (µM) (µM) (µM) 2013/11/22 10.59 31.47 9.43 1.29 15.00 8.67 1.29 3.15 0.09 2013/12/06 8.95 33.14 7.78 0.48 20.40 16.37 1.67 2.34 0.00 2013/12/20 8.50 33.40 9.72 1.31 19.60 13.15 1.43 2.91 0.04 2014/01/14 10.09 33.25 9.43 1.30 12.10 9.66 1.11 3.05 0.19 2014/01/31 10.34 33.40 9.56 1.87 13.16 12.13 1.19 2.81 0.23 2014/02/14 11.17 31.96 8.94 0.77 14.27 7.18 0.96 3.22 0.19 2014/02/28 11.14 32.47 9.22 1.55 10.99 5.57 0.75 2.02 0.13 2014/03/14 11.97 31.16 8.56 0.57 22.22 9.31 1.13 4.44 0.30 2014/03/28 10.97 32.83 8.86 1.49 24.08 13.81 1.36 3.44 0.20 2014/04/11 11.99 32.60 8.75 1.25 17.42 10.10 1.17 1.87 0.23 2014/04/25 11.29 33.27 8.75 3.09 16.17 12.46 1.35 4.09 0.30 2014/05/09 14.41 32.23 7.63 1.35 16.02 4.78 1.52 7.33 0.23 2014/05/23 14.27 33.52 7.34 2.01 17.17 5.97 1.34 5.21 0.23 2014/06/13 11.24 34.10 8.85 5.31 33.50 17.68 1.41 4.06 0.42 2014/06/27 12.72 34.26 11.89 6.39 5.24 0.21 0.33 3.92 0.03 2014/07/11 5.27 12.89 9.53 1.08 4.42 0.21 2014/07/25 14.79 34.05 8.45 4.27 17.79 4.82 1.22 6.03 0.23 2014/08/08 13.25 34.32 8.40 7.99 14.81 8.12 1.19 4.91 0.29 2014/08/22 13.51 34.43 8.16 1.22 10.44 6.73 1.25 5.47 0.23 2014/09/04 15.36 34.57 8.14 2.62 24.97 5.21 1.71 4.86 0.30 2014/09/19 15.90 34.45 8.12 0.81 17.20 1.25 1.31 7.99 0.19 2014/10/03 14.77 34.10 7.40 2.37 22.23 11.64 1.67 4.87 0.38 2014/10/24 14.95 32.02 8.13 1.10 9.69 3.89 1.11 5.70 0.25 2014/11/06 13.53 32.26 8.10 1.10 12.69 9.79 1.08 2.61 0.33

243