Characteristics of cone snail (family Conidae) populations and communities are predicted to differ depending on habitat type. In particular, high wave energy and greater exposure at low tides are posited to restrict body sizes of cones at intertidal marine benches in comparison to subtidal reefs. Here, we tested this prediction by comparing shell sizes of cone-snail species that occur at both seaward and lagoonal sites at two atolls in the Tuamotu Archipelago: Makemo and Rangiroa. At Makemo, we also compared sizes of individuals from a seaward site, sites within a small channel or “hoa” that allows water exchange between the sea and lagoon, and sites at increasing distances from the hoa for species that occurred at these sites. Although eight species with adequate sample sizes for analyses occurred at both seaward and lagoonal sites at Rangiroa, we only observed sufficient sample sizes of two species at both seaward and lagoonal sites at Makemo. All of these species exhibited significantly larger body sizes at lagoonal sites that are largely composed of subtidal reefs than at seaward sites that represent intertidal marine benches. These results support the prediction that habitat type influences the body size of cone snails. We also found that body sizes of cone snails steadily increased from the seaward site, through the hoa, and with increasing distance from the hoa in the lagoon. These results as well as our infrequent observations of small-sized individuals at lagoonal sites suggest that cone-snail larvae settle at seaward sites and individual snails migrate through hoas and contribute to recruitment of lagoonal populations.