Coho and Steelhead Smolt Outmigration from the San Geronimo Valley, Marin County, 2009

Prepared by Christopher Pincetich, Ph.D., SPAWN Watershed Biologist Todd Steiner, M.S., SPAWN Executive Director Paola Bouley, M.S., SPAWN Conservation Program Director

Ssssssssssssssssss Salmon Protection Salmon Protection And Watershed Network And Watershed PO Box 370 • Forest Knolls, CA 94933 Network Ph. 415.663.8590 • Fax 415.663.9534 PO Box 400 • Forest www.SpawnUSA.org Knolls, CA 94933

i Salmon Protection and Watershed Network (SPAWN)

Table of Contents

Abstract…………………………………………………………………………………………………...…1

Introduction……………………………………………………………….…………………….…………...1 Lagunitas Coho………………………………………….…………………………...…………...1 Lagunitas Steelhead………………………………………….…………………….…….……...2 San Geronimo Valley Headwaters………………………………………….….….…………...3 Salmon Protection and Watershed Network (SPAWN)- Background…..…………….….....4 Methods………………………..……………………………………………………………………………4 Smolt Trap Design and Location ……………………………………...………………….……5 Daily Monitoring…………………………………………………………………………..………6 Smolt Scale Collection and Age Estimation Analyses…………………………………..……7 Data Analyses……………………………………………………………………………….……7 Fulton Condition Factor……………………………………………………………..…..…….…8 Results……………………………………………………………………………………..……...…...……8 Coho Salmon………………………………………………………………………..…..……...…8 Steelhead……………………………………..……………………………………..…..…….…12 Other Aquatic Organisms ……………………………………..………………………..…...…15

Discussion………………………………………………………………………………………….…...…17 San Geronimo Valley Coho Smolt Production…………………………………..……..…....17 San Geronimo Valley Steelhead Smolt Production………………………………………… 19 San Geronimo Valley Trends…………………………………………………………………. 20

Acknowledgements…………………………………………………………………………….…………21

References……………………………………………………………………………………………...…22

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List of Tables

Table 1. Summary of coho smolt captures from San Geronimo, Arroyo, and Larsen Creeks….…9

Table 2. Summary of coho smolt measurements from the San Geronimo Valley Creek…………10

Table 3. Table 3. Summary of total steelhead smolt captures from San Geronimo, Arroyo, and Larsen Creeks…………………………………………………………………………………………….13

Table 4. Summary of measurements from San Geronimo Creek steelhead smolts with smoltification code 4. …………………………..…………………..…………………………..….….…13

Table 5. Summary of measurements from San Geronimo Creek steelhead parr with smoltification codes 2-3. ……………..…………………………………………….…………………………………....14

Table 6. Summary counts of native, non-salmonid species recovered in smolt traps……...……..15

Table 7. Summary counts of non-salmonid, non-native, invasive species that are predators on salmon eggs and fry that were recovered in smolt traps………………………………………..……16

Table 8. Summary of coho smolt population estimates from the San Geronimo Valley (SGV) and upper Lagunitas Creek Watershed (LCW). ……………………………………..………………….…17

List of Figures

Figure 1. The Lagunitas Creek watershed is located north of San Francisco Bay in Marin County, California, and originates near the top of Mount Tamalpais and flows north to Tomales Bay. The San Geronimo Creek watershed is the upper, un-dammed headwater tributary that joins Lagunitas Creek 7.2 km downstream from its origins on White’s Hill……………………...…………3

Figure 2. The San Geronimo Valley sub-watershed contains twelve main tributaries that support coho salmon or steelhead. The location of the three outmigrant smolt monitoring stations is shown along San Geronimo, Arroyo, and Larsen Creeks…………………………………..…………5

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Figure 3. The smolt traps were constructed as a combination fyke net/pipe trap design intended for larger creeks (A). Smolts were measured (B) and weighed (C) while immersed in cold creek water to minimize handling stress. …………………………………………………………………….…6

Figure 4. Outmigrant coho smolt captures, capture probability, and population estimates from 2009 monitoring in San Geronimo Creek……………………...………………………………….……10

Figure 5. Salmonid measurements from 2009 San Geronimo Creek monitoring of fork length and wet weight plotted for coho smolts …………………………….……………………………………….11

Figure 6. Length frequency histogram of coho smolts size classes captured from both San Geronimo and Larsen Creek smolt traps. …………………………….…………………………….…11

Figure 7. A representative coho smolt scale sample, under 10x magnification, that indicates an estimated age of 2+ years old for the fish……………………………………..………………………12

Figure 8. Outmigrant steelhead smolt captures, capture probability, and population estimates from 2009 monitoring in San Geronimo Creek………………………………………………....…….14

Figure 9. Salmonid measurements from 2009 San Geronimo Creek monitoring of fork length and wet weight plotted for steelhead smolts (A) and parr (B)……………………………………………14

Figure 10. In-stream creek temperatures during the outmigration monitoring were recorded at each smolt trap using an in situ HOBO device at 15 minute intervals in (A) Arroyo, (B) Larsen, and (C) San Geronimo Creeks. ……………………………………………….………………………16

Figure 11. Annual cumulative rainfall as measured in San Geronimo Creek just upstream of the smolt trap in Lagunitas indicates rainfall averages below annual averages since 2006, evidence of current drought conditions observed throughout the SGV watershed (top). Monthly rainfall before, during, and after the salmonid smolt migration for 2009(bottom)………………..………..18

iv Abstract

Smolt production of coho salmon and steelhead in the San Geronimo Valley (SGV) sub- watershed, the un-dammed headwaters of the Lagunitas Creek Watershed (LCW) in Marin County, California, was determined through outmigrant trapping during the spring months March- June 2009 by the Salmon Protection and Watershed Network (SPAWN). SPAWN biologists made daily observations and measurements at three fyke-net fish traps, one on San Geronimo Creek just before its confluence with Lagunitas Creek, and two on smaller tributaries to San Geronimo Creek. Mark and recapture analysis was used to estimate the number of coho salmon or steelhead smolts migrating toward the ocean. Coho smolt captures and population estimates calculated using DARR 2.0 software from the San Geronimo trap were the second largest in 4 years of monitoring, with 362 coho captures resulting in a population estimate of 2,499 (±370) individuals. Tributary traps produced small numbers of coho smolts, and for the first time in 4 years, no coho fry were observed in the traps. Scale samples from 11 large coho smolts from Larsen and San Geronimo Creeks were examined and indicated the presence of 9 age 2+ coho smolts, suggesting smolt migration in 2008 was inhibited by barriers to outmigration, possibly exacerbated by the driest spring and summer on record in Marin since 1879. Similar annual steelhead population responses were seen with 208 captures from San Geronimo Creek resulting in an estimated population of 1,625 (±409), the second largest population observed in the 4 years of monitoring. The value of small tributaries such as Larsen Creek was demonstrated by the 48 steelhead smolts observed outmigrating this year, almost double the numbers ever recorded from this creek. A total of 664 steelhead fry were observed from all three traps, much lower than previous years. Based on the results of monitoring conducted by MMWD, Stillwater Sciences, and SPAWN from 2006-2009, the San Geronimo Valley watershed is responsible for rearing an average of 40% of the total coho smolt population in the upper Lagunitas Creek watershed.

Introduction

The Lagunitas Creek watershed (LCW) of Marin County supports the largest-remaining, documented wild population of endangered Central Coast coho salmon (Oncorhynchus kisutch) in California (Moyle et al., 2008). The Central California Coast Evolutionarily Significant Unit (ESU) of coho salmon has been listed as endangered in the State of California and under the U.S. Endangered Species Act (ESA) since 2005. The LCW also supports a population of Central California Coast ESU steelhead (Oncorhynchus mykiss) that has been listed at threatened under the ESA since 2006.

Lagunitas Coho The LCW occupies 281.85 km2 (69,646 acres) in Marin County and contains 56.32 km (35 miles) of ESA-listed coho salmon coho bearing streams and 59.55 km (37 miles) of steelhead streams

1 Salmon Protection and Watershed Network (SPAWN) (NOAA SWFS, 2008). Coho salmon normally have a fixed three-year birth to death life cycle, producing three separate year classes each of which can be considered essentially a separate population because there is little mixing among year class lineages. Juvenile coho salmon emerge from redds in late winter to early spring and spend over one year in the stream before undergoing a physiological and morphological smoltification process and migrating to the ocean in the following spring. During smoltification, their scales slough, vertical parr marks along the lateral line fade and become a uniform silver color, their length increases in proportion to their girth, and they begin physiological adaptations to prepare them for life in seawater. They spend about 1.5 years in the ocean and return to spawn in the late fall to early winter three years from when they were spawned. The regular occurrence of “jacks” that return to spawning grounds as 2-year old males in limited numbers, and the occasional juvenile that holds over in their natal stream for 2 winters, are known exceptions to the usual fixed life-cycle of coho salmon.

Due to the relatively rigid life history of coho, monitoring coho salmon smolt numbers can provide population estimates that can be compared to juvenile and escapement population estimates for the same year class to better understand survivorship bottlenecks. Smolt outmigration monitoring, in conjunction with other life stage monitoring activities, can assist in characterizing the geographical and seasonal distribution of productivity for salmonids, and is a valuable resource for directing long-term management and restoration actions for their freshwater habitat.

Data collected through smolt trapping also has direct management utility, as it can lead to a better understanding of the environmental factors, and their timing, that result in cessation of downstream smolt movement, which may be used to determine instream restoration windows that would not impair migration of smolts (NPS SOP, 2005).

Lagunitas Steelhead Steelhead are the anadromous form of rainbow trout and have a much more flexible life history when compared to coho salmon. Adult winter-run steelhead present in the LCW typically spawn later in the winter or in early spring, and thus fry emerge from gravel redds later than coho salmon. Steelhead can delay outmigration by a year or more before undergoing the physiological and morphological maturation into a smolt and migrating to the ocean. They also can vary their time as seagoing fish, spending 0.5-2 years in the ocean before returning to spawn. Steelhead are known to be iteroparous, meaning they can make several spawning trips between fresh and salt water in their life span. Adult steelhead in the LCW typically return to spawn mid to late winter

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Although our smolt monitoring is focused on salmonid smolts migrating to the ocean, our efforts also provide additional presence, relative abundance and size measurement data for other aquatic species such as California roach and Pacific lamprey.

The San Geronimo Valley Headwaters The 24.26 km2 (5,995 acre) San Geronimo Valley (SGV) watershed drains to San Geronimo Creek which flows 7.2 km (4.5 mi) from its source on White’s Hill to the confluence with Lagunitas Creek, and contains twelve tributaries, including 1st through 3rd order sub-basins ranging in size from 0.38 to 3.8 km2 (293.9 to 939.0 acres; Figures 1&2; SWS, 2009). The five tributaries to San Geronimo Creek with the most salmonid habitat are Woodacre, Larsen, Willis Evans Canyon, Montezuma, and the Arroyo/El Cerrito/Barranca complex of creeks. The SGV is listed by the National Marine Fisheries Service in their draft “Coho Recovery Plan” as one of their top-ten high-

3 Salmon Protection and Watershed Network (SPAWN) priority “core” conservation area across the entire range for CCC ESU coho salmon (NMFS pers. comm., 2009). The LCW as a whole received the highest possible priority listing (a 5 out of 5) for directing recovery efforts for coho salmon by the CA Department of Fish and Game (CA DFG) in the “Recovery Strategy for California Coho Salmon” document (CA DFG, 2004). The SGV is extremely important habitat for coho salmon, comprising less than 9% of the total area of the LCW and in recent years supporting up to 40% of LCW coho spawning and 40% of smolt production.

The SGV is also the location of West Marin’s largest residential human population. Fifty-eight percent of the watershed area is privately owned with forty percent of these private parcels occurring directly within 100-ft of a stream, encroaching on critical riparian and floodplain habitat. Significant human impacts occur in this area impacting not only San Geronimo Creek and its tributaries, but also reaches of Lagunitas Creek downstream of this area in State and Federal lands. Current impacts of high concern include loss of riparian habitat to past land-use and continued residential development, excessive fine sedimentation due to runoff from poorly maintained roads and development, loss of winter refuge and rearing habitat, contamination of surface waters from leaking septic systems, roads, and pesticide and fertilizer applications, and loss of habitat behind migration barriers, especially road culverts.

Salmon Protection and Watershed Network (SPAWN) Background SPAWN is a community-based grassroots non-profit that has been monitoring summer habitat to relocate salmonids fry from drying pools since 1999, monitoring spawning on tributaries in the SGV since 2001, and monitoring smolt outmigration from the SGV since 2006. These efforts support and compliment the work of partners in the LCW including the CA DFG, the Regional Water Quality Control Board, National Marine Fisheries Service, Marin Resources Conservation District, National Park Service, and Marin Municipal Water District (MMWD).

Methods

Smolt production of coho salmon and steelhead in the SGV was determined during the period of March through June of 2009, with daily monitoring of traps by SPAWN biologists following California Department of Fish and Game protocols (Duffy, 2005). Monitoring was performed in coordination with additional efforts across the larger Lagunitas Creek watershed by the MMWD, Stillwater Sciences (SWS), and Point Reyes National Seashore. SPAWN’s smolt monitoring project is performed under NOAA Fisheries Authorizations and Permits for Protected Species ESA Section 10(a)(1)(A) permit (Pacific fish), Permit #1162 modification 3 scientific research and enhancement issued in 2005 and California Dept of Fish and Game Scientific Collection Permits.

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Smolt Trap Design and Location Due to occurrences of high flows on San Geronimo Creek, a combination fyke net/pipe trap (Gale 2000) trap (Figure 3). The primary pipe/fyke net trap was located in San Geronimo Creek ~500 meters upstream of the confluence of San Geronimo Creek and Lagunitas Creek and 10.8 km (6.7 miles) upstream from the outmigrant rotary screw trap operated by MMWD. The study area consisted of a wide, cobble and gravel glide with a low gradient and depth of 0.2-1.1 m. The fyke net was supported by identical, 2.5m long wood framed nets and sandbags that formed a shallow “V” into the primary funnel that spanned approximately 90% of the width of the creek. An approximately 1 m area was left open along the shallow bank to allow for upstream migration of adult steelhead, as well as movement of ducks and other aquatic species. The primary fyke net funnel opening was 1.75m feet wide and 1.75m feet tall, constructed of netting with 3 cm openings for the initial 3 meters and 0.3 cm openings for the final 3 meters of the primary funnel. The funnel terminates in a 20cm diameter plastic pipe, which connected to a 0.75m tall, 0.75m wide, and 1.25m long frame trap box covered with 2mm mesh netting. The trap box was divided into two sections by a solid frame containing 2cm metal screen to create an area approximately 25% of the trap box for fry and other small organisms to remain protected from larger fishes. In addition, a 1cm mesh panel and zippered opening was added to the back of the trap box to allow fry to pass through the trapping box without being handled when large numbers were being caught that exceeded amount allowed under permit. In situ temperature data-loggers (HOBO Pendant Temperature Logger, Onset Computer Corporation) was secured in each trap box to

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Figure 3. The smolt traps were constructed as a combination fyke net/pipe trap design intended for larger creeks (A). Smolts were weighed (B) and measured (C) while immersed in cold creek water to minimize handling stress. record in-stream temperature at 15 minute intervals through most of the study period. Two smaller fyke net traps of similar design are located in upstream tributaries of the San Geronimo Creek stationed in Arroyo Creek and Larsen Creek, at 10-80 meters upstream of their confluence with San Geronimo Creek. The locations of the 3 pipe/fyke net traps are shown in Figure 2.

Daily Monitoring Smolt traps were monitored daily early each morning beginning in March and ending in June. Captured fishes were carefully caught by hand dip-nets and transferred to clean, five-gallon buckets containing aerators and freshly collected creek water. Salmon smolts were briefly exposed to carbon dioxide as a sedative. Each fish was identified, fork length measured, weighed, and for juvenile salmonids >85mm in fork length, the degree of smoltification scored on a scale of 1-4 (1=parr, 2=early transitional, 3=late transitional, 4=smolting). Identification was performed with the assistance of “Field Identification of Coastal Juvenile Salmonids” (Pollard et al., 1997). Fork length was determined on all salmon smolts and most other fishes by carefully transferring the dip netted fish into a measuring device constructed to cradle the fish and retain water to submerge the gills when tilted, and measurements were recorded in millimeters (Figure 3, B). Wet weight of fish was measured by carefully placing netted fish into a pre-tarred weigh boat containing enough water to submerge the average sized smolt and then weighed to 0.1 gram with a Ohaus Scout Pro 600g field scale (Ohaus ,USA; Figure 3, C). Steelhead and coho were considered smolts if they were predominately silver in color, lacking clear parr marks, were loosing scales, and exceeded 85mm fork length. Salmon fry observed in the trap were often numerous and very sensitive to handling stress, and when large numbers of very small fry were observed, these fish were counted and an estimate of length for each 5mm size class was recorded.

The mark and recapture study used to generate population estimates consisted of marking all new coho and steelhead smolts (>85mm fork length, smolt codes 2-4) with a fin clip followed by 6 Salmon Protection and Watershed Network (SPAWN) upstream relocation and release. In coordination with MMWD’s downstream monitoring trap, a unique SPAWN marking clip was given to smolts each week, and the cycle of clips would repeat after four weeks. Fin clips typically consisted of a 1-2mm right-angle clip from a pair of small, sharp scissors on the rounded edge of the fin. Typical fin clip marks were the upper caudal clip, dorsal and upper caudal clip, or anal and upper caudal clip. When smolts were captured from either Larsen or Arroyo creek by SPAWN, a unique marking clip would be given to attempt the mark and recapture efficiency calculation at these locations and to track smolts migrating downstream from these tributaries to the lower San Geronimo smolt trap. Relocation of marked smolts was performed approximately 30m upstream into a large, deep pool with sufficient cover. Marked smolts that were recaptured were released approximately 20m downstream with other fishes and salmon fry into a large, deep pool with cover by natural vegetation.

During the 2009 monitoring season the three traps were operated for 13 weeks, from March 11 to June 4. However, on May 1-5, 2009, from 2-4 inches of rain fell in the San Geronimo Valley causing high flows that compromised trap conditions. Over-topping of the funnel sandbags at all 3 smolt traps, severe clogging of the funnel nets and pipes, and no steelhead and very few coho smolts were observed during this period in week 8.

Smolt Scale Collection and Age Estimation Analyses Scale samples were collected from 11 smolts over 120mm with clear smoltification and clear presence of loose scales to acquire additional life-history information. Scales were removed from above the lateral line and between the dorsal and adipose fins with gentle scraping across the body from head to tail, using the dull edge from the fin-clip scissors. This gentle scraping was repeated 2-3 times to collect approximately 6-10 individual scales. The scales were transferred to a small square of paper, which was carefully folded to encase the scales and sealed in a plastic envelope. Both the paper and plastic envelope were labeled with the date, species, location, fork length (mm), body wet weight (grams), and the initials of the person taking the sample. Scale samples were stored in a cool, dry location until analyses.

Each scale sample was observed under a 10x dissecting microscope and photographed. A determination of the number of annuli on the scale was used to estimate whether the fish was 0+, 1+, or 2+ years of age, in collaboration with Marin Municipal Water District Biologist, Eric Ettlinger. Scales with very few rings were identified as re-growth scales and discarded. Detailed notes and digital photographs were recorded to share with collaborators.

Data Analyses Due to the slight differences in smoltification code assignments during different years and the irregularity of timing of steelhead smolts and their resulting smoltification scores, the calculation of measurements for steelhead are presented separately for juveniles with smoltification codes 2-3 and smolts with a smoltification code of 4. Smolt population estimates and capture probability, or 7 Salmon Protection and Watershed Network (SPAWN) trap efficiency, were calculated using Darroch Analysis with Rank-Reduction (DARR 2.0; Bjorkstedt, 2005) analysis and was performed with the assistance of Eric Bjorkstedt at the National Marine Fisheries Service. All smolts marked with a fin clip were included in the DARR analyses, but a sufficient sample size was only collected at the San Geronimo Creek trap, so population estimates were not calculated from Larsen or Arroyo creek trap date. Coho and steelhead data sets were analyzed separately.

Fulton Condition Factor Fork length was measured and should be the principal factor affecting the weight of most fish species. However, there can be differences in weight between similar length fish of the same species within a particular watershed, within the surrounding region, or due to morphological changes occurring during smoltification. In order to compare length-weight relationships, we applied Fulton Condition Factors (K) to establish comparable indices of condition. Fulton’s condition factor is widely used in fisheries and general fish biology studies, with the intention of describing the “condition”, or relative biomass, of that individual. It is calculated from the relationship between the weight of a fish and its length. The formula for Fulton’s condition factor is: K = W /L3 where K = Fulton’s condition factor, W = the weight of the fish, and L is the length (measured as fork length). A scaling factor was applied to bring the value of K close to 1.

Results

Coho Salmon The first smolts were captured on March 11, the first day of trapping, and the final coho smolt was captured on May 29th. The San Geronimo trap produced a total of 362 individual coho smolt captures, 73 marked recaptures, resulting in a population estimate of 2,499 (±370) based on an estimated 24% recapture rate (DARR 2.0; Table 1). This should be considered a minimum estimate since smolts were captured on the first day of trapping operations and we presume we missed the earliest outmigrants.

8 Salmon Protection and Watershed Network (SPAWN) Table 1. Summary of coho smolt captures from San Geronimo, Arroyo, and Larsen Creeks*.

San San Geronimo Coho Population Year Geronimo Larsen Arroyo Trap Efficiency Estimate 2006 393 - - 23% 3,318 (±568) 2007 301 8 4 45% 1,232(±182) 2008 413 2 5 38% 1,609 (±135) 2009 362 5 0 24% 2,499 (±370)

Average 367 5 3 32.5% 2,165 (±314)

* Arroyo and Larsen Creeks were not monitored in 2006.

For captures at the San Geronimo Creek trap, the average coho smolt fork length was 109.9mm (±9.7), weight was 14.0g (±3.5), and the Fulton Condition Factor K value was 1.03 (±0.1) (Table 2) and individual data are plotted in Figures 5 & 6.

The timing of peak migration, measured from the downstream San Geronimo trap, occurred in week 7 (April 20-26) or week 8 (April 27- May 3), based on actual numbers or estimated population, respectively.

Five coho smolts were captured in the Larsen Creek trap (Table 1), with an average length of 130.6mm (±29.8), average weight of 24.7g (±11.4), and a Fulton Condition Factor of 1.03 (±0.1)(Table 2). The largest 3 coho smolts observed in 2009 were trapped in Larsen creek on May 4-5 after the high flow episode and measured 140, 150, and 151mm. No coho smolts were captured in the Arroyo Creek trap in 2009. Capture results and measurements from previous years are presented in Tables 1 & 2.

Scale samples were taken from 11 coho smolts, 10 from San Geronimo and 1 from Larsen Creek (Figure 7). Only coho smolts that appeared larger than normal size, in the range 120mm –140mm fork length, were sampled. Results of these scale sample analyses indicate that 9 of the 11 smolts were age 2+ year old coho smolts and two 120mm smolt were 1+ year old fish.

There were no coho fry observed in 2009 in either of the three traps. This can be attributed to the fact that, unlike for steelhead spawners, no coho adults were observed spawning in the San Geronimo Valley subwatershed during the winter of 2008.

9 Salmon Protection and Watershed Network (SPAWN) Table 2. Summary of coho smolt measurements from San Geronimo Valley Creeks. Coho weight Coho fork length Fulton’s Condition Factor Year (grams±STDEV) (mm±STDEV) (K±STD)

San Geronimo Creek San Geronimo Creek San Geronimo Creek 2006 14.8 (±3.6) 110.8 (±8.8) 1.07 (±0.1) 2007 14.1 (±3.8) 110.5 (±9.7) 1.03 (±0.1) 2008 12.5 (±2.6) 106.7 (±7.6) 1.02 (±0.1) 2009 14.0 (±3.5) 109.9 (±9.7) 1.03 (±0.1)

Year Larsen Creek Larsen Creek Larsen Creek 2007 13.8 (±2.1) 108.1 (±6.5) 1.09 (±0.12) 2008 13.8 108 1.09 2009 24.7 (±11.4) 130.6 (±29.7) 1.03 (±0.1)

Year Arroyo Creek Arroyo Creek Arroyo Creek 2007 11.5 (2.2) 97.8 (2.9) 1.22 (0.21) 2008 13.8 (2.8) 108 (7.9) 1.08 (0.05) 2009 - - -

San Geronimo Coho Smolts 2009 DARR

700 0.6 DARR Estimate 600 0.5 New Captures

500 Capture Probability 0.4 400 0.3 300 0.2

200 Capture Probability Number of coho smolts

100 0.1

0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Week

Figure 4. Outmigrant coho smolt captures, capture probability, and population estimates from 2009 monitoring in San Geronimo Creek.

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San Geronimo Creek coho smolt physiology

30 y = 4E-05x2.6896 25 R2 = 0.9132

10 wet weight (grams) 5

0 80 90 100 110 120 130 140 150 fork length (mm)

Figure 5. Salmonid measurements from 2009 San Geronimo Creek monitoring of fork length and wet weight plotted for coho smolts.

Length frequency of coho smolts from the San Geronimo Valley 100 90 80 70 60 50 40 30 20 number of smolts 10 0 80-85 86-90 91-95 96-100101-105106-110111-115116-120121-125126-130131-135136-140141-145146-150

fork length (mm)

Figure 6. Length frequency histogram of coho smolts size classes captured from both San Geronimo and Larsen Creek smolt traps.

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Tightly arranged rings depict slow winter growth annuli.

Figure 7. A representative coho smolt scale sample, under 10x magnification, that indicates an estimated age of 2+ years old for the fish.

Steelhead The first steelhead smolts were captured on the first day of trapping, March 11, the final steelhead smolt was captured on May 25, and the final steelhead parr was captured on May 29.

A total of 153 steelhead smolts were captured at the San Geronimo Creek trap, and the mark and recapture data was used to calculate an average 16% trap capture probability for the entire study and a population estimate of 1,625 (±409) steelhead smolts (Table 3), and should be considered a minimum estimate, based on timing of trap installation. The average fork length for steelhead smolts with clear smoltification and a smolt code of 4 was 160.0mm (±31.2), weight was 42.2g (±26.3), and the Fulton Condition Factor K value was 1.02 (±0.3) (Table 4, and Figure 8A). For steelhead parr with a smolt code of 2-3 the average fork length was 104.9mm (±14.6), weight was 13.1g (±5.4), and the Fulton Condition Factor K value was 1.09 (±0.1), (Table 5, and Figure 8B).

Peak migration timing based on actual captures, occurred in week 2 (March 16-22) with 71 steelhead smolts captured. However, the DARR 2.0 modeling software estimated peak migration population occurring in week 5 (April 6-12) (Figure 7), but is the result of the low capture sample size and recapture rates for weeks 3-13, resulting in DARR 2.0 pooling this period into one sample group.

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Table 3. Summary of total steelhead smolt captures from San Geronimo, Arroyo, and Larsen Creeks*.

San San Geronimo Steelhead Population Year Geronimo Larsen Arroyo Trap Efficiency Estimate 2006 117 - - 15% 938 (±243) 2007 160 25 8 12% 1,728 (±364) 2008 112 2 1 12% 1,112 (±310) 2009 153 48 2 16% 1,625 (±409)

Average 135 25 4 14% 1,351 (±332)

* Arroyo and Larsen Creeks were not monitored in 2006.

Table 4. Summary of measurements from San Geronimo Creek steelhead smolts with smoltification code 4.

Steelhead weight Steelhead fork length Fulton’s Condition Factor Year (grams±STDEV) (mm±STDEV) (K±STDEV) 2006 38.9 (±20.3) 152.5 (±25.8) 1.02 (±0.1) 2007 57.1 (±16.9) 179.5 (±16.1) 0.97 (±0.1) 2008 58.5 (±19.5) 180.9 (±21.1) 0.98 (±0.3) 2009 42.2 (±26.3) 160.0 (±31.2) 1.02 (±0.3)

Twenty steelhead smolts captured in Larsen Creek had an average length of 145.0mm (±18.8), weight of 35.9g (±13.6), and Fulton Condition Factor of 1.13 (±0.1). Twenty eight steelhead parr (>85mm with smolt codes 2-3) had an average length of 132.6mm (±26.0), weight was 30.2g (±16.1), and a Fulton Condition Factor of 1.19 (±0.1). An additional 7 steelhead captured in Larsen Creek did not show characteristics of parr or smolts, were not of the size range to be considered young of the year fry, and had an average length of 86.9mm (±12.0), weight was 7.5g (±2.9), and a Fulton Condition Factor of 1.10 (±0.1). A single smolt (122mm, 20.2g, 1.11 K) and a single parr (113mm, 19.1g, 1.32 K) were captured in the Arroyo Creek trap.

The San Geronimo Creek trap captured 664 steelhead fry, the Arroyo trap captured 136, and no fry were captured or observed in Larsen Creek, indicating that steelhead spawning may not have occurred in Larsen Creek in 2009.

13 Salmon Protection and Watershed Network (SPAWN) Table 5. Summary of measurements from San Geronimo Creek steelhead parr with smoltification codes 2-3.

Steelhead weight Steelhead fork length Fulton’s Condition Factor Year (grams±STDEV) (mm±STDEV) (K±STDEV) 2006 19.8 (±12.3) 116.8 (±12.3) 1.11 (±0.2) 2007 22.7 (±14.3) 123.5 (±28.0) 1.07 (±0.1) 2008 11.0 (±5.6) 98.72 (±14.8) 1.07 (±0.1) 2009 13.1 (±5.4) 104.9(±14.6) 1.09 (±0.1)

San Geronimo Steelhead Smolts 2009 DARR

500 0.2

450 DARR Estimate 0.18 400 0.16 New Captures 350 0.14

300 Capture Probability 0.12

250 0.1

200 0.08

150 0.06 Capture Probability

Number of steelhead smolts 100 0.04

50 0.02

0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Week

Figure 8. Outmigrant steelhead smolt captures, capture probability, and population estimates from 2009 monitoring in San Geronimo Creek.

San Geronimo Creek steelhead smolt San Geronimo Creek steelhead parr physiology physiology 150 35

30 125 2.9717 y = 3E-05x2.795 y = 1E-05x 25 2 100 R2 = 0.9832 R = 0.9668 20 75 15 50 10 wet weight (grams) 25 wet weight (grams) (A) 5 (B)

0 0 75 100 125 150 175 200 225 250 70 80 90 100 110 120 130 140 150 fork length (mm) fork length (mm)

Figure 9. Salmonid measurements from 2009 San Geronimo Creek monitoring of fork length and wet weight plotted for steelhead smolts (A) and parr (B).

14 Salmon Protection and Watershed Network (SPAWN) Other Aquatic Organisms In addition to salmonids, also found in the traps in 2009 were: three native fish species, Pacific lamprey ammocoetes (Lampetra tridentate), California Roach (Hesperoleucus symmetricus), and three-spined Stickleback (Gasterosteus aculeatus); and one native amphibian species, Pacific newt (Taricha sp.)(Table 6). Trap captures of non-native species included: one fish, the bluegill (Lepomis macrochirus); one amphibian, the eastern bullfrog (Rana catesbeiana); and one invertebrate, the signal Crayfish (Pacifastacus leniusculus) (Table 7).

Table 6. Summary counts of native, non-salmonid species recovered in smolt traps. Data on each species is summarized as sample size (n), mean length in millimeters (±standard deviation), and mean wet weight in grams (±standard deviation). Species Individuals Observed 2009 2008 2007 2006

n 0 1 0 1 Freshwater Sculpin Fork length - 101mm - Not measured (Cottus sp.) Weight 13.0g - Not measured n 11 1 13 11 Pacific newt (Taricha Total length 110.9mm (±43.6) 25mm 105.8mm (±17.7) 53.3mm (±20.2) sp.) Weight 12.2g (±8.1) 1.0g 9.7g (±3.1) 5.1 (±6.8) Three-spined n 76 14 12 2 Stickleback(Gasterosteu Fork length 44.7mm (±4.7) 47.2mm (±4.9) 45.3mm (±2.4) Not measured s aculeatus) Weight 1.1g (±0.5) 1.3g (±0.5) 1.1g (±0.3) Not measured

California Roach n 243 86 164 99 (Hesperoleucus Fork length 58.9mm (±21.5) 57.8mm (±16.1) 47.6mm (±24.5) 77.6mm (1±7.8)

symmetricus) Weight 4.4g (±4.0) 3.3g (±3.3) 3.4g (±5.0) 8.0g (±6.0)

Pacific lamprey n 252 246 43 90

ammocoetes (Lampetra Total length 124.3mm (±12.2) 110.9mm (±18.2) 133.2mm (±11.8) 115.9mm (±19.2)

tridentate) Weight 3.2g (±0.9) 2.5 g(±1.4) 4.4g (±1.0) 2.9g (±0.9)

In-stream Temperature In-stream creek temperatures during the outmigration monitoring were recorded at each smolt trap using an in situ HOBO device at 15-minute intervals throughout most of the study period (Figure 10). Diurnal creek temperatures varied by 2-4°C, and daytime high temperatures peaked above 16.0°C, which is above optimum temperatures for rearing coho salmonids (Welsh et al., 2001). The location of the Larsen Creek monitoring station dried up in the second week of June, ending measurements at this location while data continued to be recorded in the other creeks.

15 Salmon Protection and Watershed Network (SPAWN) Table 7. Summary counts of non-salmonid, non-native, invasive species that are predators on salmon eggs and fry that were recovered in smolt traps. Data is summarized as sample size (n), mean length in millimeters (±standard deviation), and mean wet weight in grams (±standard deviation). Species Individuals Observed 2009 2008 2007 2006

n 0 0 1 0 Louisiana crayfish Total length - - 81mm - (Procambarus clarkii) Weight - - 13g - n 13 0 0 6 Bluegill Fork length 53.5mm (±20.6) - - Not measured (Lepomis macrochirus) Weight 4.4g (±8.6) - - Not measured n 4 0 5 5 Bullfrog Total length 72.0mm (±54.7) - 128.2mm (±10.1) Not measured (Rana catesbeiana) Weight 16.6 g(±16.8) - 35.1g (±5.6) Not measured Signal Crayfish n 22 50 108 23 (Pacifastacus Total length 82.2mm(±20.6) 81.9mm (±16.6) 89.7mm (±18.8) 71.2 mm (±10.7) leniusculus) Weight 18.1g (±11.6) 22.5g (±12.5) 26.6g (±13.2) Not measured

Arroyo Creek Temperatures 2009 Larsen Creek Temperatures 2009 20.0 18.0

18.0 16.0

16.0 14.0

14.0 12.0

12.0 10.0

10.0

HOBO Temperature (deg. C) 8.0 HOBO Temperature (deg. C) 8.0 6.0 4/14 4/28 5/12 5/26 6/9 6/23 7/7 7/21 4/14 4/24 5/4 5/14 5/24 6/3 Date Date

San Geronimo Creek Temperatures 2009 22.0

20.0

18.0

16.0

14.0

12.0

10.0

HOBO Temperature (deg.C) 8.0

6.0 4/14 4/24 5/4 5/14 5/24 6/3 6/13 6/23 7/3 7/13 Date

16 Salmon Protection and Watershed Network (SPAWN)

Discussion

San Geronimo Valley Coho Salmon Production The outmigration of SGV coho in 2009 occurred primarily in April and May, identical to observations for 2006-2008, and agrees with the typical spring outmigration of coho smolts throughout the California Central Coast coho ESU (Weitkamp et. al, 1995). The peak migration of coho in 2009 occurred in week 7 (April 20-26) or week 8 (April 27- May 3), based on actual numbers or estimated population, respectively. This difference can be attributed to the high stormwater flows May 1-5, which over-topped sandbags funneling flow into the traps, resulting in reduced captures and recaptures rate. The DARR 2.0 software estimated a 16% capture probability in week 7 and 7% percent in week 8, taking actual captures of 83 coho smolts in week 7 and 47 in week 8 and determining an estimated 499 smolts in week 7 and 642 in week 8. During the 4 years of smolt monitoring performed by SPAWN, instream flow conditions have varied greatly from April through June due to seasonal storms (Balance Hydrologics Inc., personal communication). The timing of salmonid smolt outmigration has consistently peaked in late April and early May, negating any obvious connection to flow and rainfall. Additional monitoring is needed to determine if factors other than seasonal timing are responsible for the timing of coho outmigration. Based on these monitoring results, watershed managers and planners should delay any in-stream work that may impact salmonids smolt migration until mid June or later to avoid disturbance to the migration of these sensitive fish.

Table 8. Summary of coho smolt population estimates from the San Geronimo Valley (SGV) and upper Lagunitas Creek Watershed (LCW). San Geronimo Valley Upper Lagunitas Creek Year Coho DARR Estimate Watershed Coho Estimate SGV % of LCW 2006 3,318 (±568) 6,261*(±1,238) 53% 2007 1,232(±182) 2,776*(±692) 44% 2008 1,609 (±135) 6,679*(±3,745) 24% 2009 2,499 (±370) 6,373* 39% Average 2,165 5,522 40% *Reported from MMWD/Stillwater Sciences estimate, all other data calculated from DARR 2.0.

The date of our first day of trapping was coordinated with other agencies working in the watershed and resulted in immediate detection of salmonid outmigration. Future efforts should focus on beginning this monitoring earlier, if water conditions allow, to capture the entire outmigration period in our monitoring efforts. Current population estimates presented should be considered minimum estimates based on the lack of information on the exact beginning and magnitude of outmigration. Despite these minimum estimates, SGV coho smolt production accounts for a four-year average of 40% of the total upper LCW coho smolts (Table 8).

17 Salmon Protection and Watershed Network (SPAWN)

Figure 11. Annual cumulative rainfall as measured in San Geronimo Creek just upstream of the smolt trap in Lagunitas indicates rainfall averages below annual averages Monthly rainfall before, during, and after the salmonid smolt migration for 2009 (bottom).

The 2009 coho population estimate of 2,499 (+/-370) exceeds the mean estimated population (2,165 ± 314) for all years (n=4), and is the second highest estimate recorded for the SGV. This is surprising considering the poor summer conditions for this year-class due to record low rainfall and drought conditions in the spring and summer of 2008 resulted in the driest spring on record in Marin since 1879 (Figure 11: MMWD 2008). In addition, the average length, weight, and K factor increased in 2009 compared to 2008 for smolts trapped at San Geronimo, and more closely represents the values measured in 2006-2007. While the annual SGV smolt population estimate is relatively variable, the juvenile population estimates determined from summer monitoring during these same years by MMWD range from 1,842-13,098, which is much more variable. This discrepancy is currently believed to be the result of juvenile losses over winter in high-flow conditions due to a lack of sufficient high-flow refuge habitat in the SGV (SWS, 2008).

The results of scale samples confirmed the presence of 9 age 2+ coho smolts originating from both Larsen and San Geronimo Creeks. Although the scale sampling was not random and did target larger individuals with a higher likelihood of older age, it is an important discovery about the local life-history strategies of coho salmon in the SGV and indicates that drought conditions impact their outmigration as a result of strandings in drying tributaries and behind migration barriers. SPAWN’s juvenile salmonid rescue and relocation program located and relocated a 18 Salmon Protection and Watershed Network (SPAWN) coho smolt from the upper, North fork of San Geronimo Creek in August of 2008, indicating that the drought conditions in spring and summer of 2008 did produce such a rapid deterioration in habitat connectivity that coho outmigration was affected. Past summer habitat surveys and the fact that the 5 coho smolts trapped from Larsen Creek in 2009 represented extremes, with 1 measuring <85mm and 4 measuring >120mm, suggest that coho outmigration in Larsen Creek is impacted by low flows and drought conditions. The age estimates of the 9 coho in 2009 serve as further confirmation that reduced creek flows and habitat connectivity can affect coho life-history in the SGV, and could potentially impact the population as a whole. While other studies have found evidence of hold-over by coho smolts into a second winter, it is not entirely known if these 2+ year old smolts spend only one summer in the ocean or two. Monitoring outmigration further upstream of the Larsen Creek confluence, or tracking juvenile fish with radio implants, could provide more information on the current survival strategies of juvenile coho and their use of SGV tributaries.

The complete lack of coho fry observed in 2009 in either of the three traps was a first for our monitoring efforts in the SGV. This can be explained by the lack of coho adults observed to spawn in the SGV during the winter of 2008/2009. There is evidence that 2 salmonid redds may have been coho redds, but their occurrence in February overlapped with the typical steelhead spawning season and the lack of coho observed on these redds made a definitive determination impossible.

San Geronimo Valley Steelhead Smolt Production The 2009 monitoring found the second highest number of captured steelhead smolts as well as the second highest estimate of the outmigrating population since SPAWN began annual monitoring in 2006. The number of steelhead captured within Larsen Creek was almost double the second highest capture recorded (48 in 2009 vs. 25 in 2007), demonstrating the value of the tributaries to San Geronimo Creek, such as Larsen Creek. As previously mentioned, drought conditions in the spring and summer of 2008, the driest spring on record in Marin since 1879, severely impacted the SGV watershed creating fish passage barriers as flows went subsurface isolating pools with rearing salmonids. During 2008 smolt monitoring, dry conditions cut-off Larsen Creek from San Geronimo Creek as early as May 5th, approximately one month earlier than this tributary typically sees drying conditions (SPAWN, 2009). The timing of the creation of this migration barrier for steelhead smolts likely trapped previous year-class fish, and could explain the large number of steelhead moving out of Larsen Creek in 2009. Alternatively, the confluence of Larsen Creek is known to contain a large backwater eddy at high flows, and this condition could attract young of the year fish up into Larsen Creek during the winter flows to seek refuge from mainstem flows, and these fish then stayed in Larsen Creek. In 2009, 40% of the steelhead captured from Larsen Creek were observed in March, 10% in April, and 50% in May, indicating that the May 1-5 rainfall events triggered a second wave of migration. Continued habitat surveying and salmonid search operations in Larsen Creek during summer months when 19 Salmon Protection and Watershed Network (SPAWN) persistent isolation of pool habitats occur should result in a more detailed assessment of this situation.

Peak steelhead migration period occurred well before the peak coho smolt migration using both the actual catch and population estimate data in 2009 and in all previous years of monitoring (SPAWN, 2009). Steelhead smolts were captured at both the very start and ending of the monitoring, and it appears that migration has virtually ceased by the first week of June. Steelhead juveniles with smoltification codes 2-3 consistently show the highest K values (Table 5) and the strongest correlation in length to weight ratio, indicating that the San Geronimo sub-watershed habitat is very well suited for the needs of these fish. However, like coho, the smoltification of steelhead is likely to skew the length to weight relationship of these fish, making comparisons of weight and condition factor less accurate than fork length comparison.

San Geronimo Valley Trends Monitoring of salmonids in the SGV and LCW has intensified in recent years in an attempt to determine all the factors limiting salmon survival and recovery and serving to guide restoration efforts.

The drought experienced throughout California over the last 3 years is having local impacts on the habitat quality and quantity in the SGV for endangered coho. The 2009 scale age analyses have shown that some of the largest coho smolts captured were likely the result of disconnected habitat that altered typical migration timing. This habitat disconnection not only reduces the quantity of habitat, but SPAWN water quality measurements in 2008-2009 also indicate that during the summer months dissolved oxygen levels were depressed, at times below 2 mg/l dissolved oxygen at the surface of deep pools known to support salmonids. In addition, the monitoring of non-salmonid species detected a greater abundance in 2009 than any previous year in native California roach, three-spined stickleback, pacific lamprey, and the non-native bluegill. In 2009, all non-native bluegill, but for one, were observed after the high flow event of May 1-5, 11 in Larsen Creek and 2 in San Geronimo Creek, when water levels in the San Geronimo Valley Golf Course ponds had overflowed directly into Larsen and San Geronimo Creeks. Not only is this indicative of a shift towards increased abundance in fish species more tolerant of warmer water than salmonids, but also could impact the available food and habitat needed to sustain robust juvenile salmonid populations.

The LCW, including the SGV, is currently listed in the state Clean Water Act 303(d) list as impaired for sediment, nutrient, and pathogens. The under-regulated septic tanks in the SGV are a known source of nutrient and pathogen pollution, and potentially the source of additional non- point source pollutants such as pharmaceutical drugs, personal care products, and pesticide that could have sublethal impacts on salmonid migration success, reproductive success, and normal development (McCarthy et. al., 2008). Non-point source pollution effects are greatly increased 20 Salmon Protection and Watershed Network (SPAWN) with reduced dilution from seasonal low-flow and drought conditions, resulting in increased likelihood of toxic exposure levels. When combined with the inability of juvenile salmonids to escape from isolated pools, the risk of mortality due to poor water quality greatly increases.

According to a Limiting Factors Analyses conducted in 2006 on the lower LCW that assumed spawning adults and juvenile seeding were at stable maximums, the lack of high-flow refuge habitat is the primary limiting factor for salmonids in the watershed (SWS, 2008). Recommendations from the CA DFG include several habitat enhancements for the San Geronimo Valley such as an increase of in-stream wood, elimination of migration barriers, and reduction of sediment runoff from unpaved roads and trail systems (DFG, 2004). Factors hypothesized to influence juvenile salmonids include, density dependent coho growth in San Geronimo Creek, high densities of both coho and steelhead can inhibit steelhead growth, a positive correlation with juvenile steelhead estimates in San Geronimo Creek and February and March stream flows, and a conservative historical estimate of fish abundance in San Geronimo Creek glides due to recent discovery of coho smolts occupying un-surveyed glides (Ettlinger et al., 2007). However, due to decreasing escapement to the LCW and specifically the SGV spawning habitats, these habitat limiting factors must be balanced with the overall reduction of the population, that may be reaching levels below earlier assumptions and driving a new set of limiting factors.

The monitoring of outmigrating salmon smolts by SPAWN continues to result in detailed population and physiology information validating the importance of the critical habitat in the San Geronimo Valley sub-watershed in contributing to the overall coho population in the Lagunitas Creek watershed. These results suggest a population of coho and steelhead in the SGV that can potentially adapt to drought conditions and persist despite declining spawner escapement to the watershed. For the period of monitoring by both SPAWN and MMWD from 2006-2008, the SGV, which is less than 9% of the total LCW, supported and average of 40% of the total LCW estimated coho smolt population, validating the importance of continued habitat conservation, restoration and monitoring efforts in this area.

Acknowledgments

SPAWN wishes to thank our dedicated volunteers and program partners for support of this project, including Julie and NoahLani Litwin, Mel Wright, Angela Rodoni, Joe McQueeney and family, Sherry Mason, Sara Cambell, the entire SPAWN Smolt Monitoring Volunteer Team, the Marin Resources Conservation District, Gail Seymour at the California Department of Fish and Game, Americorps Watershed Stewards Project, Eric Bjorkstedt (NOAA), Eric Ettlinger and the Marin Municipal Water District, , Bella Vista Foundation, and Patagonia Foundation.

21 Salmon Protection and Watershed Network (SPAWN)

References

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22 Salmon Protection and Watershed Network (SPAWN) Pollard, W.R., G.F. Hartman, C. Groot, Phil Edgell, 1997. Field Identification of Coastal Juvenile Salmonids. Harbour Publishing, British Columbia, Canada.

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Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, G. B. Milner, D. J. Teel, R. G. Kope, and R. S. Waples. 1995. Statue review of coho salmon form Washington, Oregon, and California. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-24. * Welsh, Hartwell H. JR., Garth R. Hodgson, Bret C. Harvey, 2001. Distribution of Juvenile Coho Salmon in Relation to Water Temperatures in Tributaries of the Mattole River, California. North American Journal of Fisheries Management 21:464-470, 2001