Benthic marine populations are often replenished by a combination of larvae from local and distant sources. To promote retention of locally spawned larvae in strong, unidirectional boundary current systems, benthic marine organisms must utilize biophysical mechanisms to minimize advective loss. We examined patterns in larval fish abundance, age distribution, and assemblage in relation to environmental variables in the Straits of Florida to better understand the factors underlying larval transport and retention in a boundary current system. Depth was the primary structuring element; larval assemblages were more distinct across vertical distances of tens of metres than they were over horizontal distances of tens to hundreds of kilometres. However, depth distributions were species-specific, and larval assemblages inside and outside of mesoscale eddies were distinct. Age distributions were consistent with the hypothesis that mesoscale eddies provide opportunities for retention. Our data indicate that the effect of eddies on larval retention is likely taxon-specific and temporally variable, as synchronization of reproductive output, larval distribution, and timing of eddy passage are prerequisite to entrainment and subsequent retention of locally spawned larvae.