We capitalized on a long-term record of larval recruitment and a distinctive oceanographic signature to reveal how changes in ocean conditions affect larval advection, behavior, and recruitment in a region of strong, persistent upwelling and recruitment limitation. We repeatedly sampled the vertical and horizontal distribution of a larval assemblage and ocean conditions during infrequent relaxations of prevailing upwelling winds near Bodega Bay, California. During prolonged relaxation events, a poleward, coastal, boundary current imported low-salinity surface waters that were devoid of larvae to the study area. The resident larval assemblage was restricted to cold, saline, bottom waters and pushed offshore while diel vertical migrations were suppressed. Hence, changes in oceanographic conditions strongly affected behaviorally mediated larval distributions, revealing the reason that few species recruit during relaxation events in this region. During relaxation events in upwelling regions, poleward coastal boundary currents will force larvae offshore throughout the water column at small headlands and in seaward-flowing bottom currents at straight coastlines, but recruitment may decrease markedly only near estuaries where few larvae will arrive in low-salinity surface waters. Targeted profiling of larval assemblages complements widespread monitoring of recruitment from shore and is necessary to determine how changing ocean conditions affect larval distributions, recruitment dynamics, and the connectivity of populations.