In the California Current Ecosystem (CCE), krill represent a key link between primary production and higher trophic level species owing to their central position in the food web and tendency to form dense aggregations. However, the strongly advective circulation associated with coastal upwelling may spatiotemporally decouple the occurrence and persistence of krill hotspots from phytoplankton biomass and nutrient sources. Results from a physical-biological model provide insights into fundamental mechanisms controlling the phenology of krill hotspots in the CCE and their sensitivity to alongshore variations in primary production and ocean currents. The model solution indicates that dynamics controlling krill hotspot formation, intensity and persistence are strongly heterogeneous and must be understood in the context of local alongshore variations in coastal upwelling, modulated by regional circulation patterns. Furthermore, the model suggests that regions promoting krill aggregations in the CCE coincide with increased observed abundances of key marine mammal and seabird species.