San Francisco Estuary and Watershed Science

California’s variable hydroclimate is projected to become increasingly volatile in the 21st century. Yet, there is widespread recognition that extreme events, such as record-breaking heatwaves and catastrophic wildfires, are already becoming the new normal. The 2025 edition of the State of Bay–Delta Science (SBDS) presents the current state of the science on climate change and extreme events affecting the Delta and its watershed, and in doing so, generates new insights on knowledge gaps and promising directions for future research. In this essay we present five perspectives to advance science-informed decision-making in the era of climate change and extreme events. To meet these challenges, Delta scientists and decision-makers can leverage the many effective practices that are already in place, such as long-term monitoring programs, collaborative synthesis venues, science-informed decision-making processes, and Tribal and community partnerships. New and sophisticated tools that harness big data are helping to streamline information flows to scientists. Open science practices are facilitating greater collaboration and improving access to more integrated datasets and to models that link different parts of the system. These assets have strengthened innovation and learning across the Delta. Nevertheless, serious challenges remain. Climate change signals can be difficult to detect as a result of the variable hydroclimate. Greater levels of uncertainty as a result of evolving climate models can present challenges for decision-making. Looking forward, the Delta scientific system can help maintain its relevance to natural resource management by strengthening its capacity for collaborative, open, and actionable science. Such an emphasis is required for anticipating and responding to the new climate and weather realities of the 21st century.

Flooding in the Bay–Delta is most commonly due to runoff from atmospheric river (AR) storms, often enhanced by low-elevation snowmelt. In this paper, we review the current science of ARs and their projected enhancement in a warming climate. We also address the changing state of the Sierra Nevada snowpack. Climate-model projections indicate increasing contributions to extreme precipitation from ARs, and more variable hydroclimate, with increased floods as well as droughts. Observations, meanwhile, do not yet show enhanced precipitation intensity trends. In agreement with climate-model projections, observations do show that, as the climate continues to warm, California’s greatest natural freshwater reservoir—its snowpack—continues to erode. This is despite record snowpacks (e.g., 2023) still being possible, and potentially exacerbating flood effects from ARs in a highly variable hydroclimate. Original analysis of extreme historical and projected precipitation events shows events of the magnitude associated with the New Year 1997 floods are expected to become twice as likely by the late 21st century. Moreover, as extreme precipitation events are expected to become wetter, hydrologic modeling suggests that extreme runoff events will be disproportionately enhanced, primarily as the result of a greater fraction of rain vs. snow. We also discuss the mitigating influence of water management on extreme flows, and mention new research results, challenges, and opportunities associated with sub-seasonal and seasonal precipitation predictability. We suggest that—along with infrastructural modernization, as well as maintenance and improvement of observational networks—current and future challenges for water management can be mitigated by better and longer lead-time weather and climate-forecast information.

Global change affects the forests and wildlands of California through rising temperatures, earlier snowmelt, more rain and less snow, greater vapor-pressure deficits, and forest dieback, resulting in increased frequency, size, and severity of wildfires. California has experienced its eight largest wildfires since 1932 in the period from 2018 to 2024. The largest fire to date (August Complex Fire) occurred in 2020—a year in which 1.7 million ha or 4% of California’s land area burned—and burned 418,000 ha. These mega-fires (>10,000 ha) can severely affect water quality and aquatic ecosystems. Water-quality variables affected by wildfire include temperature, sediment load, turbidity, dissolved oxygen, pH, redox potential, soluble and particulate organic carbon, nutrients, metals, natural- and human-produced organic contaminants, and primary/secondary producers. Wildfire and water interact at watershed scales, with water-quality impairments responding linearly with the percentage of the watershed area burned, and responding exponentially as burn severity increases. Vegetation recovery is key to the duration of water-quality effects, and short-term, post-fire weather dictates actual water-related effects. Urban areas are hot spots for the production and transport of water pollutants such as sediments, heavy metals, mercury, nutrients, and toxic organic compounds. Water-treatability challenges after wildfire include short-term odor and taste, increased sediment and turbidity, and increased total and dissolved organic matter. Implications for water quality from catastrophic wildfire on downstream reservoirs are important research needs because ~80% of California’s water supply passes through reservoirs before use. Notably, there is a crucial need for development and assessment of post-fire, land-management practices to mitigate adverse water-quality effects. Finally, continuous measurements of water quality are critical to document the severity and duration of episodic pulses of wildfire-sensitive constituents that are mobilized and transported to aquatic ecosystems after catastrophic mega-fires.

Fish losses to entrainment in water diversions in the Sacramento–San Joaquin Delta have been a long-standing conservation concern. We evaluated Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) entrainment risk associated with the Barker Slough Pumping Plant (BSPP) by integrating hydrodynamic, growth, survival, and fish-screen-selectivity information into indices of entrainment risk for nine locations in the Cache Slough Complex (CSC). Our fundamental question was: How does risk of entrainment into BSPP vary in space and time? We found the predicted risk of entrainment into BSPP is extremely high from the adjacent Lindsey Slough. From elsewhere in the CSC, entrainment risk into BSPP is approximately zero in both wet and dry years, such that local irrigation diversions are the only potential source of entrainment loss. We estimated Delta Smelt outgrow vulnerability to entrainment through the BSPP fish-screens in 35 to 53 days while Longfin Smelt remain vulnerable for 90 to 98 days. Research indicates some impingement is probable even after fish outgrow risk of being entrained through the screens if they continue to be passively transported. Our entrainment indices sometimes deviated considerably from hydrodynamic transport predictions within Lindsey Slough because larval fish have high natural mortality rates and, at least for Delta Smelt, growth rates high enough to modify the transport predictions. Since 1989, the predicted entrainment risk at BSPP has declined in the winter but increased in April through May as a result of long-term trends in how much water is seasonally diverted at BSPP. If the one-dimensional model we used to estimate fish transport is accurate, then Delta Smelt and Longfin Smelt would need to be spawned in Barker or Lindsey sloughs to face a meaningful risk of entrainment at BSPP. This conclusion does not appear to be affected by Yolo Bypass flow as had been hypothesized previously.

Freshwater inflow is vital for the ecological health of estuaries. Understanding historical flow volume and timing is therefore essential for sustainable management and restoration of these environments. Using legacy hydrologic data—including riverine water-level measurements, watershed runoff estimates, and wetland reclamation records—we extended a monthly time-series of freshwater inflow to San Francisco Estuary by 6 decades, back to California’s Gold Rush era. This period marks the onset of significant anthropogenic modifications to the waterscape. Our analysis of the extended series, normalized to unimpaired runoff, reveals an increasing trend in systemwide water use that was preceded by a decline in the latter half of the 19th century. We hypothesize this decline resulted from reduced evapotranspiration as a result of vegetation removal and reduced overbank flows from levee construction. These findings align with earlier research that shows similarities between natural and contemporary long-term annual average inflow, comparing pre-development conditions to those of the early 20th century and today. Monthly flow trends, however, displayed more nuanced, season-specific effects of human modifications. Despite unusually wet hydrology during the reconstruction period, our findings comprise an important contribution to ongoing dialogue on ecosystem-restoration targets.