A high-salinity embayment located near Beaufort, North Carolina was surveyed to create a bathymetric profile of the main basin. To examine population dynamics and habitat use within the embayment, over 3,000 blue crab locations, sex, size, and egg stage were recorded during nocturnal low tides. Males and females partitioned habitat, with males concentrated in the shallower upper portion of the embayment, and mature females concentrated near the deeper mouth of the embayment. Juvenile females were predominantly found in shallower areas within mature male habitat. Location of ovigerous crabs varied with egg developmental stage. Crabs with late-stage eggs were found closest to the mouth of the embayment, and 92.9% (156 of 168) of ovigerous crabs left the embayment before larval release and may not have returned. Because the embayment is homogenous at 35 psu, a salinity gradient is not the primary mechanism underlying this segregation. We hypothesize that tidal activity rhythms and microhabitat selection contribute to the observed spatial patterns.