Exchanges of fish larvae between the inner continental shelf and estuaries can be critical to the functional significance of these habitats as nurseries. We sampled near-surface fishes on the inner continental shelf off New Jersey and in an adjacent estuary during the summer and fall of 2005 and 2006 to evaluate the occurrence and variation in these connections. Very few of the abundant taxa (Anchoa mitchilli, Brevoortia tyrannus, Urophycis regia, Etropus microstomus, Peprilus triacanthus, and Pomatomus saltatrix) were exclusive to either habitat but some did change in relative habitat affinity among seasons. For some species, this was indicative of a departure from the ocean for estuaries (e.g., Micropogonias undulatus) while others used both habitats during the summer and fall (e.g., Syngnathus fuscus, Scophthalmus aquosus, and A. mitchilli). Together, these observations confirm the high degree of connectivity between the near-surface larval fishes from the inner continental shelf and estuaries.