SAN FRANCISCO ESTUARYESTUARYESTUARY&WAT & WATERSHED&WATERSHEDERSHED Published for the San Francisco Bay-Delta SCIENCEScience Consortium by the John Muir Institute of the Environment SAN FRANCISO ESTUARY & WATERSHED SCIENCE VOLUME 2, ISSUE 2 MAY 2004 ARTICLE 1 Spatial and Temporal Variability of Suspended-sediment Concentration in A Shallow Estuarine Environment Catherine A. Ruhl and David H. Schoellhamer ARTICLE 2 Trends in the Sediment Yield of the Sacramento River, California, 1957 – 2001 Scott A. Wright and David H. Schoellhamer ARTICLE 3 Biology and Population Dynamics of Sacramento Splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: A Review Peter B. Moyle, Randall D. Baxter, Ted Sommer, Ted C. Foin, and Scott A. Matern Copyright © 2004 by the authors, unless otherwise noted. This article is part of the collected publications of San Francisco Estuary and Watershed Science. San Francisco Estuary and Watershed Science is produced by the eScholarship Repository and bepress. MAY 2004 SAN FRANCISCO ESTUARYESTUARYESTUARY&WAT & WATERSHED&WATERSHEDERSHED Published for the San Francisco Bay-Delta SCIENCEScience Consortium by the John Muir Institute of the Environment Spatial and Temporal Variability of Suspended-sediment Concentration in a Shallow Estuarine Environment Catherine A. Ruhl and David H. Schoellhamer U.S. Geological Survey, Sacramento, California ABSTRACT concentrations in the channel were not affected; how- ever, wind played a crucial role in the resuspension of Shallow subembayments respond differently than deep sediments in the shallows. Despite wind-wave sedi- channels to physical forces acting in estuaries. The U.S. Geological Survey measured suspended-sediment ment resuspension in Honker Bay, tidally averaged concentrations at five locations in Honker Bay, a shal- suspended-sediment flux was controlled by the flood- low subembayment of San Francisco Bay, and the dominated currents. adjacent channel to investigate the spatial and tempo- KEYWORDS ral differences between deep and shallow estuarine environments. During the first freshwater pulse of the Suspended sediment, spatial variability, temporal wet season, the channel tended to transport suspended variability, wind waves, freshwater pulse, sediments through the system, whereas the shallow San Francisco Bay. area acted as off-channel storage where deposition would likely occur. Following the freshwater pulse, SUGGESTED CITATION suspended-sediment concentrations were greater in Honker Bay than in the adjacent deep channel, due to Ruhl CA, Schoellhamer DH. 2004. Spatial and tempo- the larger supply of erodible sediment on the bed. ral variability of suspended-sediment concentration in However, the tidal variability of suspended-sediment a shallow estuarine environment. San Francisco concentrations in both Honker Bay and in the adja- Estuary and Watershed Science [online serial]. Vol. 2, cent channel was greater after the freshwater pulse Issue 2 (May 2004), Article 1. than before. During wind events, suspended-sediment http://repositories.cdlib.org/jmie/sfews/vol2/iss2/art1 Ruhl and Schoellhamer: Spatial and Temporal Variability of Suspended-Sediment Concentrations MAY 2004 INTRODUCTION studied (Figure 1). Shallow estuarine environments such as Suisun Bay are ecologically significant Estuaries commonly include deeper channels and because a large fraction of the biota depends on shallower shoals or subembayments. Most sediment these areas for shelter and nourishment (Cloern and transport studies of estuaries have focused on the others 1985; Caffrey and others 1998). Suspended deeper channels because these serve as the primary sediments are an important component of the estuar- conduit of sediment between the watershed and ine environment harboring a nutrient supply, impact- ocean (see review by Uncles 2002). Sediment trans- ing light penetration through the water column, and port in shoals and subembayments, however, will dif- adsorbing potential contaminants (Cloern 1987; fer from that in deeper channels because of greater Domagalski and Kuivila 1993). wind wave resuspension, proximity to shore and trib- utaries, and greater relative benthic filtering of the In this paper, we present observed spatial and sea- shallower water column. If the tidal and tidally-aver- sonal patterns of SSC variability that indicate that aged exchange between deeper channels and neigh- shallow estuarine environments respond differently boring shoals is sufficiently large, variability in one to physical forces than neighboring deep channel can not be explained without considering variability environments. Honker Bay is somewhat independent in the other. Wind wave resuspension in shallower of the adjacent channel and tends to act as a tempo- water can be transported to the neighboring deep rary off-channel storage zone for sediments washed channel and increase suspended-sediment concentra- down during early winter storms, whereas the chan- tions (SSC) during ebb tide and less turbid water nels along the spine of San Francisco Bay tend to from the deep channel can move onto adjacent transport the sediments farther down-estuary. shoals during flood tide (Jing and Ridd 1996; Another difference between these two environments de Jonge and van Beusekom 1995; Schoellhamer is the effect of wind waves on SSC; wind waves suc- 1996). In the Tay Estuary, sediment transport from cessfully resuspend sediments in shallow areas but shallow waters during ebb tide creates turbidity max- have little effect on SSC in the deep channels ima in the deeper channel (Weir and McManus 1987). (de Jonge and van Beusekom 1995). Transport from shallow water can also change the composition of suspended sediment in a deep chan- 122 00'00" 121 57'30" 121 55'00" nel; Edelvang and Austen (1997) observed fecal pel- Grizzly EXPLANATION lets from shoals in the adjacent deep channel at the Bay DEEP WATER AREA, Mean Lower Low Water > 2M end of ebb tide. In these cases, the deeper channel SHALLOW WATER AREA, Mean Lower Low Water < 2M and shoal are communicating with one another. In S u isu SAMPLING SITE this paper, we compare SSC measurements in a deep- n Cu LONG-TERM MONITORING to er channel and adjacent subembayment that demon- 38 05'00" Ryer ff STATION Island back strate much less communication, suggesting a some- what independent subembayment. Honker Bay hdol S s p ha cmid o ll o San Francisco Bay includes extensive shallow areas, ow n b b Sui a ill Cr sun r hs2 ee with approximately one-half of its surface area being B k a y Chipps Island less than 2 m deep (Conomos and others 1985). However, the deep channels along the spine of the 38 02'30" bay are sampled most regularly for physical, chemi- Suisun Bay Meteorological Station Mallard Island cal, and biological parameters (Buchanan and Ruhl Mallard Island continuous 2000; Edmunds and others 1997; Webster and others monitoring station 1998). To investigate the spatial and temporal vari- 0 1 2 MILES ability of SSC in shallow-water areas and deep-water 0 1 2 KILOMETERS channels, Honker Bay, a shallow subembayment of Location of study area and sampling sites San Francisco Bay, and the adjacent channel were Figure 1. Produced by eScholarship Repository 3 San Francisco Estuary and Watershed Science Vol. 2, Iss. 2 [May 2004], Art. 1 SAN FRANCISCO ESTUARY & WATERSHED SCIENCE SITE DESCRIPTION The objective of the second deployment, from April AND DATA COLLECTION through August 1997, was to monitor the changes in Honker Bay is located at the eastern side of San SSC during low flows and increased wind. Not all of Francisco Bay covering approximately 10 km2, most the data collected are presented in this paper, due to of which is less than 2 m in depth. Suspended sedi- biological fouling, equipment failure, and other prob- ments throughout San Francisco Bay are comprised lems that invalidated the data. predominantly of silts and clays. Two major features Sites back and cmid were located in the shallowest of Honker Bay are a bar at the mouth of the bay, and interior parts of Honker Bay with sensors collecting Spoonbill Creek, which connects the head of the bay data approximately 0.5 m from the bed. Sites hdol to Suisun Bay east of Mallard Island (Figure 1). Very and hs2 were located on the boundary of Honker Bay little exchange occurs across the shallow bar at the with water depths of approximately 4 m and 7 m, mouth of Honker Bay, and the dominant tidal cur- respectively; the sensors collected data at approxi- rents run parallel to the bar. Additionally, the orien- mately 3 m and 0.5 m from the bed, respectively. The tation of Honker Bay is such that the currents are long-term monitoring station at Mallard Island is strongly flood-dominant (Lacy 2000). Tidally aver- located on the south side of the Suisun Bay channel aged flow through Spoonbill Creek is typically north- at a depth of approximately 13.5 m. The sensor is ward; however, southward flows through Spoonbill attached to a float and measures SSC 1 m below the Creek can occur due to wind setup and a water level water surface. A second sensor collects SSC data differential between the head of Honker Bay and the approximately 1.5 m above the bottom; however due eastern side of Suisun Bay (Warner and others 1997). to instrument problems and fouling, there are signifi- Freshwater discharge and wind are two seasonal cant periods of missing data during the study and the forcing mechanisms affecting SSC in San Francisco data will not be presented. Concentrations measured Bay. Most precipitation occurs from December to at the lower sensor are higher than those measured April, causing short duration peaks in freshwater by the upper sensor; however, the patterns and flow and increases in SSC. Baseline freshwater dis- responses to the physical forces discussed here are charge into the bay is greatest during the spring consistent between the two sensors. months, as a result of runoff from snowmelt. About Each shallow-water deployment package included a 90% of the discharge into the bay is from the velocity meter and a conductivity-temperature-depth Sacramento-San Joaquin River Delta, which drains (CTD) probe with an additional channel programmed the Central Valley of California (Smith 1987).