Broadcast-spawning marine organisms with long pelagic larval duration are often expected to be genetically homogeneous throughout their ranges. When genetic structure is found in such taxa, it may be in the form of chaotic genetic patchiness: i.e. patterns that might seem independent of any underlying environmental variation. The joint analysis of population genetic data and marine environmental data can elucidate factors driving such spatial genetic diversity patterns. Using meso-scale sampling (at a scale of 10s to 100s of km), microsatellite data and advection connectivity simulations, we studied the effect of temperate southern Australian ocean circulation on the genetic structure of the snail Nerita atramentosa. This species has a long pelagic larval duration and is represented as a single metapopulation throughout its ~3000 km range, but even so, we found that its dispersal potential is lower than expected. Connectivity simulations indicate that this is a result of the larvae that remain on the continental shelf (where currents are erratic and often shoreward) returning to the coast in much larger numbers than larvae that become entrained in the region's shelf-edge boundary currents. Our study contributes to the growing evidence that departures from the expectations of panmixia along continuous and environmentally homogeneous coastlines are not limited to low-dispersal species, and it identifies on-shelf larval retention as an important factor limiting dispersal.