Abstract Extreme events reshape ocean ecosystems with significant implications for nutrient and carbon cycling. Here, we demonstrate that flooding on land can be a significant driver of biogeochemical variability in the open ocean, even in relatively dry climates. Using satellite observations, in situ measurements, and Lagrangian particle tracking, we present evidence that freshwater discharge from extreme precipitation during the 2023 water year was transported into the oligotrophic region of the California Current System. This transport was facilitated by submesoscale eddies and filaments and resulted in significant anomalies in surface salinity, stratification, nutrient concentrations, as well as phytoplankton and bacterioplankton community composition. These observations highlight the importance of episodic river discharge events in shaping offshore biogeochemical fluxes and ecosystem structure in eastern boundary current systems. With more frequent atmospheric river events projected, the likelihood of observing these specific hydrographic and biogeochemical conditions may be increasing.