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Abstract We analyzed impacts of the 2014–2015 Pacific Warm Anomaly and 2015–2016 El Niño on physical and biogeochemical variables at two southern California Current System moorings (CCE2, nearshore upwelling off Point Conception; CCE1, offshore California Current). Nitrate and Chl‐afluorescence were <1 μM and <1 Standardized Fluorescence Unit, respectively, at CCE2 for the entire durations of the Warm Anomaly and El Niño, the two longest periods of such low values in our time series. Negative nitrate and Chl‐aanomalies at CCE2 were interrupted briefly by upwelling conditions in spring 2015. Near‐surface temperature anomalies appeared simultaneously at both moorings in spring 2014, indicating region‐wide onset of Warm Anomaly temperatures, although sustained negative nitrate and Chl‐aanomalies only occurred offshore at CCE1 during El Niño (summer 2015 to spring 2016). Warm Anomaly temperature changes were expressed more strongly in near‐surface (<40 m) than subsurface (75 m) waters at both moorings, while El Niño produced comparable temperature anomalies at near‐surface and subsurface depths. Nearshore Ω_aragoniteat 76 m showed notably fewer undersaturation events during both warm periods, suggesting an environment more conducive to calcifying organisms. Planktonic calcifying molluscs (pteropods and heteropods) increased markedly in springs 2014 and 2016 and remained modestly elevated in spring 2015. Moorings provide high‐frequency measurements essential for resolving the onset timing of anomalous conditions and frequency and duration of short‐term (days‐to‐weeks) perturbations (reduced nitrate and aragonite undersaturation events) that can affect marine organisms.