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During 2014 exceptionally warm water temperatures developed across a wide area off the California coast and within San Francisco Bay (SFB) and persisted into 2016. Observations and numerical model output are used to document this warming and determine its origins. The coastal warming was mostly confined to the upper 100 m of the ocean and was manifested strongly in the two leading modes of upper ocean (0–100 m) temperature variability in the extratropical eastern Pacific. Observations suggest that the coastal warming in 2014 propagated into nearshore regions from the west while later indicating a warming influence that propagated from south to north into the region associated with the 2015–2016 El Niño event. An analysis of the upper ocean (0–100 m) heat budget in a Regional Ocean Modeling System (ROMS) simulation confirmed this scenario. The results from a set of sensitivity runs with the model in which the lateral boundary conditions varied supported the conclusions drawn from the heat budget analysis. Concerning the warming in the SFB, an examination of the observations and the heat budget in an unstructured‐grid numerical model simulation suggested that the warming during the second half of 2014 and early 2016 originated in the adjacent California coastal ocean and propagated through the Golden Gate into the Bay. The finding that the coastal and Bay warming are due to the relatively slow propagation of signals from remote sources raises the possibility that such warming events may be predictable many months or even several seasons in advance.

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Over the past 15 years, the development and application of multi-dimensional hydrodynamic models in San Francisco Bay and the Sacramento-San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system. Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta under future conditions. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship among X2, flow, fish abundance, and the low salinity zone. Through the coupling of multi-dimensional models with wind wave and sediment transport models, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms in the estuary, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta. This paper provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multi-dimensional models to predict how future Delta conditions will affect both fish and water supply.

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