San Francisco Bay

Sacramento-San Joaquin Delta Historical Ecology Investigation: Exploring Pattern and Process

San Francisco Estuary Institute (SFEI) | September 12th, 2012

In 2012, SFEI researchers (in collaboration with the CA Department of Fish and Wildlife) completed a historical ecology study of the Sacramento-San Joaquin Delta. The

In 2012, SFEI researchers (in collaboration with the CA Department of Fish and Wildlife) completed a historical ecology study of the Sacramento-San Joaquin Delta. The project improves understanding of what the Delta looked like and how it functioned prior to the significant modification that has occurred over the last 160 years. This historical reconstruction documents patterns of variation and extent of habitat types throughout the Delta for improved understanding of species support functions and controlling physical processes within the native landscape. Knowing how different parts of the vast historical Delta looked and functioned provides needed information for future restoration strategies.

Sacramento/San Joaquin Delta Dilemma

Assembly Office of Research (AOR) | January 1st, 1982

Sailing the Salt Line

Bay Nature | July 2nd, 2024

A strait is a place of motion. Change is a constant in our universe, a fact we humans often struggle with, but certain places are especially good at reminding us of it. T

A strait is a place of motion. Change is a constant in our universe, a fact we humans often struggle with, but certain places are especially good at reminding us of it. The Carquinez Strait itself was only just born, some 560,000 years ago—explosively, according to one theory—when a giant inland lake forced a path to the ocean. This created the unusual inverted river delta (with the fan pointing inland, instead of spreading out onto the coast) that is the San Francisco Bay.

Salinity Changes the Dynamics of Pyrethroid Toxicity in Terms of Behavioral Effects on Newly Hatched Delta Smelt Larvae

Toxics (MDPI) | February 20th, 2021

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases w

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases with increasing salinity, potentially increasing the risk of exposure for aquatic organisms at higher salinities. In the San Francisco Bay Delta (SFBD) estuary, pyrethroid concentrations increase during the rainy season, coinciding with the spawning season of Delta Smelt (Hypomesus transpacificus), an endangered, endemic fish. Furthermore, salinity intrusion in the SFBD is exacerbated by global climate change, which may change the dynamics of pyrethroid toxicity on aquatic animals. Therefore, examining the effect of salinity on the sublethal toxicity of pyrethroids is essential for risk assessments, especially during the early life stages of estuarine fishes. To address this, we investigated behavioral effects of permethrin and bifenthrin at three environmentally relevant concentrations across a salinity gradient (0.5, 2 and 6 PSU) on Delta Smelt yolk-sac larvae. Our results suggest that environmentally relevant concentrations of pyrethroids can perturb Delta Smelt larvae behavior even at the lowest concentrations (<1 ng/L) and that salinity can change the dynamic of pyrethroid toxicity in terms of behavioral effects, especially for bifenthrin, where salinity was positively correlated with anti-thigmotaxis at each concentration.

Salinity Incursion and Water Resources, Appendix to Bulletin No. 76, Delta Water Facilities

California Department of Water Resources (DWR) | April 16th, 1962

Data and analyses contained in this appendix were utilized to determine the present and future quantity and quality of water supplies within the Delta and to determine

Data and analyses contained in this appendix were utilized to determine the present and future quantity and quality of water supplies within the Delta and to determine the conditions under which the State Water Facilities must operate within the Delta with the various facilities proposed in Bulletin No. 76 constructed therein. In general, the conditions imposed result from conservative assumptions of available water supply and Delta channel hydraulics.

Salt Water Problem: San Francisco Bay and Delta of Sacramento and San Joaquin Rivers

Association of Industrial Water Users of Contra Costa and Solano Counties | April 12th, 1928

PENETRATION OF SALT WATER IN UPPER BAY AND LOWER RIVER REGiON Under natural conditions, Carquinez Straits marked, approximately, the boundary between salt and fresh

PENETRATION OF SALT WATER IN UPPER BAY AND LOWER RIVER REGiON Under natural conditions, Carquinez Straits marked, approximately, the boundary between salt and fresh water in the upper San Francisco Bay and delta region of the two tributary rivers-the Sacramento and San Joaquin. Ordinarily salt water was present below the straits and fresh water was present above. Native vegetation in the tide marshes was predominantly of salt water types around San Pablo Bay and of fresh water types around Suisun Bay. In tidal waters, into which run fresh water streams of variable flow, there is an ebb and flow of salt water and the zone of mixing will move up and down stream as the fresh water flow increases and decreases. For short intervals in late summer of years of minimum flow, salt water penetrated the lower river and delta region, and in wet seasons the upper bay was fresh, part of the time, to the Golden Gate. This variation in quality of water was not, however, of sufficient duration to affect the characteristic vegetation growth of the regions on each side of the straits, nor to change the designation of Suisun Bay as ordinarily a fresh water body and San Francisco Bay as salt water. The works of man have changed conditions in many ways. The most important changes have been brought about gradualJy,-so slowly as to be hardly noticeable. The dry season of 1918,-when large summer diversions for irrigation in the Sacramento Valley resulted in the sudden penetration of salt water farther upstream than ever known before, at such an early period in summer first brought the salt water problem to public notice. The slow effects of increasing diversions in previous years had escaped notice, but were brought prominently to the attention of the inhabitants of the upper bay and delta regions in this year. Since 1918, the dry years of 1920, 1924- and 1926 have more convincingly demonstrated the importance of the salt water problem. An accurate picture of natural conditions is not possible, because no records have been collected on which such a picture can be based, but very close approximations can be made. The log of the distance traveled by the water barge of the California Hawaiian Sugar Company in going upstream to obtain fresh water has been kept since 1908. These figures give the means of determining approximately the conditions during that period. In 1908 irrigation had been extensively developed in both valleys and conditions then were not natural. For an estimate of earlier conditions we must go to the stream flow records of the tributary streams before important diversions are taken out. It is the practice of the Sugar Company to send the barge upstream until water of approximately 50 to 70 parts per million chlorine is reached. The crew of the barge are equipped with apparatus by which water is analyzed until this degree of purity is reached. Since trips are made nearly every day during the summer months, the record is a very good indication of the point reached by salt water. A summary of the complete records shows the fluctuation of the line between fresh and salt water. Records of the Sugar Company arc attached. (Table 1.) The Sugar Company requires water of great purity. For irrigation, domestic or ordinary industrial uses, water of a lesser degree of purity may be used. A comparison of the point where the Sugar Company's barge is filled with the point where the remaining uses could be satisfied, indicates that from five to ten miles downstream from the place where the barge turns, water could be obtained satisfactory for domestic supply. Making an allowance of 7 1/2 miles in the average records, we find that an average flow of 5,000 second feet in both streams will maintain fresh water at Collinsville; 7,000 second feet will maintain fresh water at the San Francisco-Sacramento ferry. If we sum up the flow of the important tributaries of the Sacramento and San Joaquin rivers at the points where these streams leave the mountains and assume that this flow under natural conditions would have reached the head of the Suisun Bay we will find that at no time in the past ten years would the average monthly flow have been Jess than 5,100 second feet. It is probable, should all streams be running in a natural way, that salt water would have penetrated no farther in this extremely dry period than Antioch, and then only for a few days at a time. It is not possible to make a more detailed study of this condition without making a number of assumptions as to speed of flow from the gaging stations to the head of the bay, and there is little accurate information on which the assumptions may be made. The definite statement that salt water under natural conditions did not penetrate higher upstream than the mouth of the river, except in the driest years and then only for a few days at a time, is warranted. (See Table 2 for monthly flow of tributary streams.) At present salt water reaches Antioch every year, in two-thirds of the years running further upstream. It is to be expected that it will continue to do so in future, even in years of greatest runoff. In other words, the penetration of salt water has become a permanent phenomenon in the lower river region.

Sampling and Analysis Plan for 2016 RMP Status and Trends Bird Egg Monitoring

San Francisco Estuary Institute (SFEI) | February 1st, 2016

The samples will be collected by staff at the USGS Western Ecological Research Center [USGS-WERC] who will procure all necessary egg collection permits. Eggs will then be

The samples will be collected by staff at the USGS Western Ecological Research Center [USGS-WERC] who will procure all necessary egg collection permits. Eggs will then be analyzed for: ● Total mercury (THg) (cormorant eggs at Moss Landing Marine Laboratory-Marine Pollution Studies Lab [MLML-MPSL]; tern eggs at USGS-WERC),  ● Selenium (cormorant and tern eggs at MLML-MPSL),  ● PCBs (cormorant eggs at the California Department of Fish & Wildlife’s Water Pollution Control Laboratory [DFW-WPCL]),  ● PBDEs (cormorant eggs at DFW-WPCL) (NOTE: PBDE analysis in tern eggs was discontinued due to increased USGS costs),  ● PFCs and precursors (cormorant eggs at AXYS Analytical Laboratories), and  ● Halogenated carbazoles (cormorant eggs at Southern Illinois University) NOTE: Carbazole analyses will be done pro bono by SIU for research purposes. Carbazoles are not part of the RMP Status and Trends design. SIU will not measure percent moisture in its samples. Therefore, it is important to make sure that sample weights, prior to analysis, are accurately measured since we will be applying the percent moisture values from other laboratories to their samples. Available data will be used to back-calculate fresh wet weight values for these samples. 

Sampling and Analysis Plan for Microplastic Monitoring in San Francisco Bay and Adjacent National Marine Sanctuaries

San Francisco Estuary Institute (SFEI) | May 31st, 2017

Plastic in the ocean, and more specifically microplastic (particles <5 mm), has been gaining global attention as a pervasive and preventable threat to the health of m

Plastic in the ocean, and more specifically microplastic (particles <5 mm), has been gaining global attention as a pervasive and preventable threat to the health of marine ecosystems. Microplastic is ingested by marine organisms (Wright et al. 2013), and may impact their physiological processes (von Moos et al. 2012; Cole et al. 2013, 2015; Rochman et al. 2013, 2014b; Wright et al. 2013; Watts et al. 2015; Lu et al. 2016; Sussarellu et al. 2016). Microplastic may also contain harmful chemicals such as flame retardants, plasticizers, or dyes (Browne et al. 2013; Fries et al. 2013; Rochman et al. 2013, 2014 a,b), and may provide a substrate for the adsorption of other harmful chemicals in the ocean, like PCBs and DDT (Teuten et al. 2007), which then may be transferred up the food chain (e.g., Farrell and Nelson 2013; Rochman et al. 2014a; Setala et al. 2014). Many scientific questions remain, however, and there is a need for research on the patterns of distribution and uptake of microplastic by organisms in their ocean ecosystems.

San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report

San Francisco Estuary Institute (SFEI) | March 2nd, 2017

In 2000, the USEPA published Water Quality Standards; Establishment of Numeric Objectives for Priority Toxic Pollutants for the State of California, commonly known as the

In 2000, the USEPA published Water Quality Standards; Establishment of Numeric Objectives for Priority Toxic Pollutants for the State of California, commonly known as the California Toxics Rule (CTR), which established numeric water quality standards for 126 priority pollutants. Under the Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bays, and Estuaries of California (also known as the State Implementation Policy, SIP) the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) is required to establish water quality-based effluent limitations in order to achieve priority pollutant standards. For the purposes of this document “water quality criteria” (WQCs) will be used to refer both to the CTR established numeric criteria for 126 priority pollutants as well as to numeric objectives for 12 of these priority pollutants and tributyltin previously established in the San Francisco Bay Water Quality Control Plan (Basin Plan) and/or the National Toxics Rule. A number of these pollutants previously were or continue to be regularly monitored as part of the Regional Monitoring Program Status and Trends (RMP S&T). The priority pollutants not routinely included in RMP S&T were previously monitored in wet and dry season ambient water sampling in 2002 and 2003. Results of that effort are detailed in a previously issued report: http://www.sfei.org/documents/san-francisco-bay-ambient-monitoring-interim-report Most of the priority pollutants were not detected in that study, or detected at concentrations below their WQC. Among the pollutants that were detected, a number of them were also found at similar concentrations in lab blanks, suggesting they might not have been present (or at least were at lower concentrations) in the ambient environment. Since over a decade had passed since that previous monitoring effort, the RMP embarked on an effort to repeat measurement of these seldom analyzed (non- S&T) contaminants, to ensure conditions have not changed appreciably to present greater risk for any of them.

San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report

San Francisco Estuary Institute (SFEI) | February 1st, 2017

In 2000, the USEPA published Water Quality Standards; Establishment of Numeric Objectives for Priority Toxic Pollutants for the State of California, commonly known as t

In 2000, the USEPA published Water Quality Standards; Establishment of Numeric Objectives for Priority Toxic Pollutants for the State of California, commonly known as the California Toxics Rule (CTR), which established numeric water quality standards for 126 priority pollutants. Under the Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bays, and Estuaries of California (also known as the State Implementation Policy, SIP) the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) is required to establish water quality-based effluent limitations in order to achieve priority pollutant standards. For the purposes of this document “water quality criteria” (WQCs) will be used to refer both to the CTR established numeric criteria for 126 priority pollutants as well as to numeric objectives for 12 of these priority pollutants and tributyltin previously established in the San Francisco Bay Water Quality Control Plan (Basin Plan) and/or the National Toxics Rule. A number of these pollutants previously were or continue to be regularly monitored as part of the Regional Monitoring Program Status and Trends (RMP S&T). The priority pollutants not routinely included in RMP S&T were previously monitored in wet and dry season ambient water sampling in 2002 and 2003. Results of that effort are detailed in a previously issued : Most of the priority pollutants were not detected in that study, or detected at concentrations below their WQC. Among the pollutants that were detected, a number of them were also found at similar concentrations in lab blanks, suggesting they might not have been present (or at least were at lower concentrations) in the ambient environment. Since over a decade had passed since that previous monitoring effort, the RMP embarked on an effort to repeat measurement of these seldom analyzed (non- S&T) contaminants, to ensure conditions have not changed appreciably to present greater risk for any of them.