California's 5-year drought has ended, even as its aftermath lingers. From 2012-2016 much or all of California was under severe drought conditions, with greatly diminished precipitation, snowpack, and streamflow and higher temperatures. Water shortages to forests, aquatic ecosystems, hydroelectric power plants, rural drinking water supplies, agriculture, and cities caused billions of dollars in economic losses, killed millions of forest trees, brought several fish species closer to extinction, and caused inconvenience and some expense to millions of households and businesses. The drought also brought innovations and improvements in water management, some of which will better prepare California for future droughts. This paper summarizes the magnitude and impacts of the 2012-2016 California drought. The paper then reviews innovations arising from the drought in the larger historical context of water management in California. Lessons for California and for modern drought management are then discussed. Droughts in modern, well-managed water systems serving globalized economies need not be economically catastrophic, but will always have impacts and challenges, particularly for native ecosystems. In California and every other water system, droughts usefully expose weaknesses and inadequate preparation in water management. In this regard for California, managers of ecosystems and small rural water supplies had the most to learn.

This paper reviews what has been learned about Delta Smelt and its status since the publication of The State of Bay-Delta Science, 2008 (Healey et al. 2008). The Delta Smelt is endemic to the upper San Francisco Estuary. Much of its historic habitat is no longer available and remaining habitat is increasingly unable to sustain the population. As a listed species living in the central node of California's water supply system, Delta Smelt has been the focus of a large research effort to understand causes of decline and identify ways to recover the species. Since 2008, a remarkable record of innovative research on Delta Smelt has been achieved, which is summarized here. Unfortunately, research has not prevented the smelt's continued decline, which is the result of multiple, interacting factors. A major driver of decline is change to the Delta ecosystem from water exports, resulting in reduced outflows and high levels of entrainment in the large pumps of the South Delta. Invasions of alien species, encouraged by environmental change, have also played a contributing role in the decline. Severe drought effects have pushed Delta Smelt to record low levels in 2014-2015. The rapid decline of the species and failure of recovery efforts demonstrate an inability to manage the Delta for the "co-equal goals" of maintaining a healthy ecosystem and providing a reliable water supply for Californians. Diverse and substantial management actions are needed to preserve Delta Smelt.

The Delta Smelt Hypomesus transpacificus is a small translucent fish that lives in the heart of California's water distribution system. It is an endemic species that is on verge of extinction, largely because it is in direct competition with people for water. This article discusses the controversy surrounding this fish by describing (1) the biology of Delta Smelt; (2) California's complex water storage and distribution system; (3) the history of Delta Smelt, including conservation efforts; (4) the present controversies surrounding it; and (5) the future of Delta Smelt. The decline of Delta Smelt is a strong indicator that the ecosystem of the Sacramento–San Joaquin Delta has undergone large‐scale changes that make it an unfavorable environment for native fishes. Reversing the trajectory of the Delta Smelt toward extinction will require major shifts in California water policy and water use as well as active management of the smelt's habitat and life history.

Mortality of planktonic populations is difficult to determine because assumptions of the methods are rarely met, more so in estuaries where tidal exchange ensures violation of the assumption of a closed or spatially uniform population. Estuarine plankton populations undergo losses through movement from productive regions, creating a corresponding subsidy to regions that are less productive. We estimated mortality rates of the copepod Pseudodiaptomus forbesi in the San Francisco Estuary using a verticallife-table approach with a Bayesian estimation method, combined with estimates of spatial subsidies and losses using a spatial box model with salinity-based boundaries. Data came from a long-term monitoring program and from three sample sets for 1991-2007 and 2010-2012. A hydrodynamic model coupled with a particle-tracking model supplied exchange rates between boxes and from each box to several sinks. In situ mortality, i.e., mortality corrected for movement, was highly variable. In situ mortality of adults was high (means by box and sampling program 0.1-0.9 day −1 ) and appeared invariant with salinity or year. In situ mortality of nauplii and copepodites increased from fresh (~0) to brackish water (means 0.4-0.8 day −1 ), probably because of consumption by clams and predatory copepods in brackish water. High mortality in the low-salinity box was offset by a subsidy which increased after 1993, indicating an increase in mortality. Our results emphasize the importance of mortality and spatial subsidies in structuring populations. Mortality estimates of estuarine plankton are feasible with sufficient sampling to overcome high variability, provided adjustments are made to account for movement.

Many fishes in the San Francisco Estuary have suffered declines in recent decades, as shown by numerous long-term monitoring programs. A long-term monitoring program, such as the Interagency Ecological Program, comprises a suite of surveys, each conducted by a state or federal agency or academic institution. These types of programs have produced rich data sets that are useful for tracking species trends over time. Problems arise from drawing conclusions based on one or few surveys because each survey samples a different subset of species or reflects different spatial or temporal trends in abundance. The challenges in using data sets from these surveys for comparative purposes stem from methodological differences, magnitude of data, incompatible data formats, and end-user preference for familiar surveys. To improve the utility of these data sets and encourage multi-survey analyses, we quantitatively rate these surveys based on their ability to represent species trends, present a methodology for integrating long-term data sets, and provide examples that highlight the importance of expanded analyses. We identify areas and species that are under-sampled, and compare fish salvage data from large water export facilities with survey data. Our analysis indicates that while surveys are redundant for some species, no two surveys are completely duplicative. Differing trends become evident when considering individual and aggregate survey data, because they imply spatial, seasonal, or gear-dependent catch. Our quantitative ratings and integrated data set allow for improved and better-informed comparisons of species trends across surveys, while highlighting the importance of the current array of sampling methodologies.

The invasive aquatic plant Egeria densa (Brazilian waterweed) is a submersed aquatic plant that has expanded its distribution in both its native and introduced range. Because the plant grows so densely, it can become a problem for management of waterways and habitat restoration projects. It is difficult to remove once established and mechanical and chemical controls have shown limited effectiveness. Here we analyze the distribution of E. densa in the Sacramento-San Joaquin Delta (the Delta) of California, USA, using environmental variables that include mean water velocity, mean water turbidity, and water column depth. We found that increasing water column depth strongly limited E. densa occurrence, especially when depth at mean lower low water (MLLW) exceeds 2 m. The highest probability of occurrence occurred at locations with a water column depth of-1 to 2 m at MLLW. Turbidity had a reliably negative effect on E. densa occurrence; as water clarity has increased in the Delta, it has likely favored the spread of the plant. Neither mean water velocity nor maximum water velocity had a reliable effect on E. densa probability, in spite of scientific and observational evidence that it is sensitive to flows. These results suggest potentially serious problems with restoration projects that emphasize shallow water habitat in the range favored by E. densa. Without some way to manage spread of the plant-through spraying, sediment loading, or gating-channels in such projects are at risk of being taken over by E. densa. However, these results should be interpreted in light of the fact that water outflow in water year 2008 was very low, and that E. densa abundance may be partially controlled by higher water flows than those considered here.

No abstract

Transport time scales are common metrics of the strength of transport processes. Water age is the time elapsed since water from a specific source has entered a study area. An observational method to estimate water age relies on the progressive concentration of the heavier isotopes of hydrogen and oxygen in water that occurs during evaporation. The isotopic composition is used to derive the fraction of water evaporated, and then translated into a transport time scale by applying assumptions of representative water depth and evaporation rate. Water age can also be estimated by a hydrodynamic model using tracer transport equations. Water age calculated by each approach is compared in the Cache Slough Complex, located in the northern San Francisco Estuary, during summer conditions in which this region receives minimal direct freshwater inflow. The model's representation of tidal dispersion of Sacramento River water into this backwater region is evaluated. In order to compare directly to isotopic estimates of the fraction of water evaporated ("fractional evaporation") in addition to age, a hydrodynamic model-based property tracking approach analogous to the water age estimation approach is proposed. The age and fractional evaporation model results are analyzed to evaluate assumptions applied in the field-based age estimates. The generally good correspondence between the water age results from both approaches provides confidence in applying the modeling approach to predict age through broader spatial and temporal scales than are practical to assess using the field method, and discrepancies between the two methods suggest aspects of both approaches that may be improved. Model skill in predicting water age is compared to skill in predicting salinity. Compared to water age, salinity observations are shown to be a less useful diagnostic of transport in this low salinity region in which salt inputs are poorly constrained.