ABSTRACT: In order to effectively manage a fishery, it is important to know the essential habitats used by all life history stages of the species being managed. However, this is often a challenge for animals such as the American horseshoe crab Limulus polyphemus, whose juvenile stages are difficult to find and quantify. Visual surveys and suction sampling have been used in previous studies, but in the Great Bay Estuary, New Hampshire, they are less effective, and so little is known about the habitats occupied by juvenile horseshoe crabs in this area. To fill this knowledge gap, we used SCUBA-dive surveys to locate juvenile horseshoe crabs. We found them on subtidal and some intertidal mudflats in the upper regions of the estuary, both adjacent to, and at some distance from, known spawning beaches. However we did not find them in either intertidal or subtidal areas adjacent to spawning beaches just 1-2 km closer to the coast. These data should be useful for future conservation efforts designed to protect essential horseshoe crab habitats in the Great Bay and other similar estuaries.