The 2015–2016 El Niño is by some measures one of the strongest on record, comparable to the 1982–1983 and 1997–1998 events that triggered widespread ecosystem change in the northeast Pacific. Here we describe impacts of the 2015–2016 El Niño on the California Current System (CCS) and place them in historical context using a regional ocean model and underwater glider observations. Impacts on the physical state of the CCS are weaker than expected based on tropical sea surface temperature anomalies; temperature and density fields reflect persistence of multiyear anomalies more than El Niño. While we anticipate El Niño‐related impacts on spring/summer 2016 productivity to be similarly weak, their combination with preexisting anomalous conditions likely means continued low phytoplankton biomass. This study highlights the need for regional metrics of El Niño's effects and demonstrates the potential to assess these effects before the upwelling season, when altered ecosystem functioning is most apparent.

Large‐scale patterns of positive temperature anomalies persisted throughout the surface waters of the North Pacific Ocean during 2014–2015. In the Southern California Current System, measurements by our sustained network of underwater gliders reveal the coastal effects of the recent warming. Regional upper ocean temperature anomalies were greatest since the initiation of the glider network in 2006. Additional observed physical anomalies included a depressed thermocline, high stratification, and freshening; induced biological consequences included changes in the vertical distribution of chlorophyll fluorescence. Contemporaneous surface heat flux and wind strength perturbations suggest that local anomalous atmospheric forcing caused the unusual oceanic conditions.

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The data-assimilating California State Estimate (CASE) enables the explicit evaluation of spatiotemporally varying volume and heat budgets in the coastal California Current System (CCS). An analysis of over 10 years of CASE model output diagnoses the physical drivers of the CCS mean state, annual cycles, and the 2014-16 temperature anomalies associated with a marine heat wave and an El Niño event. The largest terms in the mean mixed layer (from250 to 0 m) volume budgets are upward vertical transport at the coast and offshore-flowing ageostrophic Ekman transport at the surface, the two branches of the coastal upwelling overturning cell. Contributions from onshore geostrophic flow in the Southern California Bight and alongshore geostrophic convergence in the central CCS balance the mean volume budgets. The depthdependent annual cycle of vertical velocity exhibits the strongest upward velocity between 240and 230-m depth in April. Interannual volume budgets show that over 50% of the 2013.5-16.5 time period experienced downwelling anomalies, which were balanced predominantly by alongshore transport convergence and, less often, by onshore transport anomalies. Mixed layer temperature anomalies persisted for the entirety of 2014-16, reaching a maximum of 138 in October 2015. The mixed layer heat budget shows that intermittent high air-sea heat flux anomalies and alongshore and vertical heat advection anomalies all contributed to warming during 2014-16. A subsurface (from 2210 to 2100 m) heat budget reveals that in September 2015 anomalous poleward heat advection into the Southern California Bight by the California Undercurrent caused deeper warming during the 2015/16 El Niño.

A data-constrained state estimate of the southern California Current System (CCS) is presented and compared with withheld California Cooperative Oceanic Fisheries Investigations (CalCOFI) data and assimilated glider data over 2007–17. The objective of this comparison is to assess the ability of the California State Estimate (CASE) to reproduce the key physical features of the CCS mean state, annual cycles, and interannual variability along the three sections of the California Underwater Glider Network (CUGN). The assessment focuses on several oceanic metrics deemed most important for characterizing physical variability in the CCS: 50-m potential temperature, 80-m salinity, and 26 kg m−3 isopycnal depth and salinity. In the time mean, the CASE reproduces large-scale thermohaline and circulation structures, including observed temperature gradients, shoaling isopycnals, and the locations and magnitudes of the equatorward California Current and poleward California Undercurrent. With respect to the annual cycle, the CASE captures the phase and, to a lesser extent, the magnitude of upper-ocean warming and stratification from late summer to early fall and of isopycnal heave during springtime upwelling. The CASE also realistically captures near-surface diapycnal mixing during upwelling season and the semiannual cycle of the California Undercurrent. In terms of interannual variability, the most pronounced signals are the persistent warming and downwelling anomalies of 2014–16 and a positive isopycnal salinity anomaly that peaked with the 2015–16 El Niño.