The occurrence and potential effects of current-use pesticides are of concern in the San Francisco Estuary watershed but our understanding of the spatial and temporal distribution of contamination is limited. This paper summarizes almost two decades of historical data and uses it to describe our current knowledge of the processes controlling the occurrence of current-use pesticides in the watershed. Monitoring studies analyze fewer than half of the pesticides applied in the watershed and most of our knowledge is about inputs of dissolved pesticides in the upper watershed. The four major seasonal patterns of riverine inputs of pesticides to the estuary can be identified by usage and transport mechanism. Dormant spray insecticides applied to orchards and herbicides applied to a variety of crops are transported by rainfall during the winter. Alfalfa pesticides are detected following rainfall and irrigation return flow in the spring, and rice pesticides are detected following release of rice field water in the summer. Irrigation return flows transport a variety of herbicides during the summer. In addition, pesticides applied on Delta islands can cause elevated pesticide concentrations in localized areas. Although not as well characterized, urban creeks appear to have their own patterns of insecticide concentrations causing toxicity throughout most of the year. Current-use pesticides have also been detected on suspended and bed sediments throughout the watershed but limited data make it difficult to determine occurrence patterns. Data gaps include the lack of analysis of many pesticides (or degradates), changing pesticide use, limited information on pesticide transport within the Delta, and an incomplete understanding of the transport and persistence of sediment-associated pesticides. Future monitoring programs should be designed to address these data gaps.

Legacy and current-use contaminants enter into and accumulate throughout the San Francisco Bay−Delta (Bay−Delta), and are present at concentrations with known effects on species important to this diverse watershed. There remains major uncertainty and a lack of focused research able to address and provide understanding of effects across multiple biological scales, despite previous and ongoing emphasis on the need for it. These needs are challenging specifically because of the established regulatory programs that often monitor on a chemical-by-chemical basis, or in which decisions are grounded in lethality-based endpoints. To best address issues of contaminants in the Bay−Delta, monitoring efforts should consider effects of environmentally relevant mixtures and sub-lethal impacts that can affect ecosystem health. These efforts need to consider the complex environment in the Bay−Delta including variable abiotic (e.g., temperature, salinity) and biotic (e.g., pathogens) factors. This calls for controlled and focused research, and the development of a multi-disciplinary contaminant monitoring and assessment program that provides information across biological scales. Information gained in this manner will contribute toward evaluating parameters that could alleviate ecologically detrimental outcomes. This review is a result of a Special Symposium convened at the University of California−Davis (UCD) on January 31, 2017 to address critical information needed on how contaminants affect the Bay−Delta. The UCD Symposium focused on new tools and approaches for assessing multiple stressor effects to freshwater and estuarine systems. Our approach is similar to the recently proposed framework laid out by the U.S. Environmental Protection Agency (USEPA) that uses weight of evidence to scale toxicological responses to chemical contaminants in a laboratory, and to guide the conservation of priority species and habitats. As such, we also aimed to recommend multiple endpoints that could be used to promote a multi-disciplinary understanding of contaminant risks in Bay−Delta while supporting management needs.