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In the California Current System, cross‐shore transport of upwelled, nutrient‐rich waters from the coastal margin to the open ocean can occur within intermittent, submesoscale‐to‐mesoscale features such as filaments. Time‐varying spatial gradients within filaments affect net cross‐shore fluxes of physical, biological, and chemical tracers but require high‐resolution measurements to accurately estimate. In June 2017, theCalifornia Current EcosystemLong Term Ecological Research program process cruise (P1706) conducted repeat sections by an autonomousSprayglider and a towed SeaSoar to investigate the role of one such coastal upwelling feature, the Morro Bay filament, which was characterized by enhanced cross‐filament gradients (both physical and biological) and an along‐filament jet. Within the jet, speeds were up to 0.78 m/s and the offshore transport was 1.5 Sverdrups (3.8 Sverdrups) in the upper 100 m (500 m). A climatological data product from the sustained California Underwater Glider Network provided necessary information for water mass differentiation. The analysis revealed that the cold, salty side of the filament carried recently upwelled California Undercurrent water and corresponded to higher chlorophyll‐afluorescence than the warm, fresh side, which carried California Current water. Thus, there was a convergence of heterogeneous water masses within the core of the filament’s offshore‐flowing jet. These water masses have different geographic origins and thermohaline characteristics, which has implications for filament‐related cross‐shore fluxes and submesoscale‐to‐mesoscale biological community structure gradients.

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⁻³isopycnal 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.