San Francisco Estuary and Watershed Science

The introduced yellowfin goby (YFG) is now common throughout the tidal portion of the Sacramento-San Joaquin River system. We investigated its habitat use, size and diet in the Mokelumne River, an eastern tributary to the system. Catch per unit effort (CPUE) by boat electrofishing was significantly higher in the fall than all other seasons sampled over four years. Habitat type, turbidity and dissolved oxygen were not significantly related to CPUE between years and seasons. Temperatures were negatively related to CPUE in fall sampling only. Delta outflow and CPUE showed a significant negative relationship. Fish captured ranged from 27 mm SL (standard length) (33 mm TL (total length)) to 155 mm SL (196 mm TL) (mean 113 mm SL (138 mm TL)), with largest fish captured during the fall. Seasonal and annual analysis showed a diet composed of a variety of macroinvertebrates, including chironomids, gammarids, aquatic isopods and ephemeropterans with no difference in composition among seasons or years. The YFG’s generalist diet gives it an advantage as a successful invader, but salinity requirements appear to limit its expansion potential.

The objective of this study was to evaluate the potential sources of pesticides to the Yolo Bypass, including those that could potentially impact critical life stages of resident fish. To assess direct inputs during inundation, pesticide concentrations were analyzed in water and suspended and bed sediment samples collected from source watersheds during high-flow events. To understand inputs from direct application on fields, pesticides were also measured in soils collected from several sites within the Bypass. Thirteen current-use pesticides were detected in water samples collected in 2004 with the highest pesticide concentrations observed at the input sites to the Bypass during high-flow. Hexazinone and simazine were detected at all sites and at some of the highest concentrations. In bed and suspended sediments collected in 2004 and 2005, thirteen current-use pesticides were detected along with DDT and its metabolites. Trifluralin, DDE, and DDT were highest in the bed sediments, whereas oxyfluorfen and thiobencarb were highest in the suspended sediments. With the exception of the three organochlorine insecticides, suspended sediments had higher pesticide concentrations compared to bed sediments, indicating the potential for pesticide transport especially during high-flow events. Soil samples were dominated by DDT and its degradates but also contained a variety of current-use pesticides typically at lower concentrations. The types of pesticides detected in water and sediments were correlated with agricultural application in each watershed.

Understanding the distribution of pesticides between the water and sediment is important in assessing their fate and transport within the Bypass, and in evaluating the exposure and potential effects to resident fish.

Climate over the watershed of the San Francisco Bay Delta estuary system varies on a wide range of space and time scales, and affects downstream estuarine ecosystems. The historical climate has included mild to severe droughts and torrential rains accompanied by flooding, providing important lessons for present-day resource managers. Paleoclimate records spanning the last 10,000 years, synthesized across the Estuary, watershed and key regions beyond, provide a basis for increased understanding of how variable California’s climate can be and how it affects the Bay Delta system.

This review of paleoclimate records reveals a gradual warming and drying in California from about 10,000 years to about 4,000 years before present. During this period, the current Bay and Delta were inundated by rising sea level so that by 4,000 years ago the Bay and Delta had taken on much of their present shape and extent. Between about 4,000 and 2,000 years ago, cooler and wetter conditions prevailed in the watershed, lowering salinity in the Estuary and altering local ecosystems. Those wetter conditions gave way to increasing aridity during the past 2,000 years, a general trend punctuated by occasional prolonged and severe droughts and occasional unusually wet, cool periods. California’s climate since A.D. 1850 has been unusually stable and benign, compared to climate variations during the previous 2,000 or more years. Thus, climate variations in California’s future may be even more (perhaps much more) challenging than those of the past 100 years. To improve our understanding of these past examples of climate variability in California, and of the linkages between watershed climate and estuarine responses, greater emphases on paleoclimate records in and around the Estuary, improved temporal resolutions in several record types, and linked watershed-estuary paleo-modeling capabilities are needed.

Protected evolutionarily significant units (ESUs) of salmonids require objective and measurable criteria for guiding their recovery. In this report, we develop a method for assessing population viability and two ways to integrate these population-level assessments into an assessment of ESU viability. Population viability is assessed with quantitative extinction models or criteria relating to population size, population growth rate, the occurrence of catastrophic declines, and the degree of hatchery influence. ESU viability is assessed by examining the number and distribution of viable populations across the landscape and their proximity to sources of catastrophic disturbance.

Central Valley spring-run and winter-run Chinook salmon ESUs are not currently viable, according to the criteria-based assessment. In both ESUs, extant populations may be at low risk of extinction, but these populations represent a small portion of the historical ESUs, and are vulnerable to catastrophic disturbance. The winter-run Chinook salmon ESU, in the extreme case, is represented by a single population that spawns outside of its historical spawning range. We are unable to assess the status of the Central Valley steelhead ESU with our framework because almost all of its roughly 80 populations are classified as data deficient. The few exceptions are those populations with a closely associated hatchery, and the naturally-spawning fish in these streams are at high risk of extinction. Population monitoring in this ESU is urgently needed.

Global and regional climate change poses an additional risk to the survival of salmonids in the Central Valley. A literature review suggests that by 2100, mean summer temperatures in the Central Valley region may increase by 2-8°C, precipitation will likely shift to more rain and less snow, with significant declines in total precipitation possible, and hydrographs will likely change, especially the the southern Sierra Nevada mountains. Warming at the lower end of the predicted range may allow spring-run Chinook salmon to persist in some streams, while making some currently utilized habitat inhospitable. At the upper end of the range of predicted warming, very little spring-run Chinook salmon habitat is expected to remain suitable.

In spite of the precarious position of Central Valley salmonid ESUs, there are prospects for greatly improving their viability. Recovering Central Valley ESUs may require re-establishing populations where historical populations have been extirpated (e.g., upstream of major dams). Such major efforts should be focused on those watersheds that offer the best possibility of providing suitable habitat in a warmer future.