Aggregations of larvae of marine benthic invertebrates occur near physical and biological features of the water column, and can be the result of hydrodynamics, larval behavior, or a combination of the two. In this study, we examined the effect of flow on the vertical distribution of 4-arm larvae of the sea urchin Lytechinus variegatus relative to a halocline. In the absence of flow, the larvae did not cross but aggregated at and below haloclines in which the salinity of the bottom layer was 31 and that of the top layer was either 21 or 25. To test the effect of flow on this response, we generated a salt wedge in a 17 m flume, with 2 water layers of different salinity and opposite mainstream flow. Using the same treatments as in the absence of flow, we found that larval aggregation occurred below the halocline under low horizontal flow velocities. We propose that in the presence of laminar sheared flow, the larval vertical distribution relative to a halocline is modified by shear, which retains larvae near the halocline, resulting in a decreased probability of entrainment into the water layer of lower salinity.