Understanding the interactions among biological and physical processes is essential to determining how the environment affects transport and survival of fishes. We examined vertical distribution in larval Atlantic menhaden (Brevoortia tyrannus) and Atlantic croaker (Micropogonias undulatus) using 126 depth stratified tows in Delaware Bay, USA, during two cruises, in December 2007 and February 2008. Menhaden larvae were 16.8–24.6 and 20.5–26.2 mm standard length in December and February. Corresponding lengths for croaker were 9.3–17.9 and 8.6–19.6 mm. Using empirical observations, and statistically derived models, we explored larval concentration for both species as a function of location, depth, diel period, tidal period, size, and pairwise interactions. Menhaden concentration was best modeled as a function of station, cruise, and interactions between depth and size as well as between station and cruise. No significant differences in larval menhaden concentration were present among tidal and diel periods. Croaker concentration was best modeled as a function of size and interactions between station and diel period, depth and size, cruise and size. Despite tidal period not emerging as a significant model parameter, we observed larger croaker larvae during nighttime flood tides. Our statistical models are consistent with processes of up‐estuary transport for both species, suggesting larvae are increasingly affected by behavioral responses as larvae grow, exhibiting stronger patterns in vertical distribution. The results refine our understanding of the potential importance of size‐related differences in vertical distribution for larval transport in these species. Future research should examine the interactions among size‐specific vertical migratory capabilities, vertical distribution, transport, and retention.