While there are numerous studies of Limulus polyphemus (Atlantic Horseshoe Crab) populations on the East and Gulf coasts of the US, especially for spawning adults in large estuaries such as Delaware Bay, there are fewer efforts relative to small estuaries in the Mid-Atlantic Bight. We determined, for the first time, the pattern of seasonal linkages between the Great Bay–Little Egg Harbor estuaries in southern New Jersey and the adjacent inner continental shelf with multiple gears over multiple years. Adults of both sexes are distributed along the inner continental shelf in all seasons, while large juveniles were most abundant in the fall. The seasonal occurrence of larvae, small juveniles, and spawning adults in high salinity, sandy, natural habitats in these small estuaries was consistent. Our findings suggest that these and other small estuaries may provide the same habitats, predators, prey, and fishery resources as larger estuaries, except at a smaller scale. Thus, small estuaries contribute by enhancing landscape and habitat diversity for this vulnerable species. Further clarification of the importance of estuarine habitats would benefit from an increasing emphasis on juveniles and their subsurface habitats in small and large estuaries.