To document nest survival and habitat differences in the nesting habitats of Clapper Rails (Rallus longirostis) in tidal marshes of the northern Gulf of Mexico, we monitored 76 active nests within the Pascagoula River Marsh Coastal Preserve (a freshwater-dominated estuary) and the Grand Bay National Estuarine Research Reserve (a marine-influenced estuary) in coastal Mississippi from 2005 to 2007. During 2006, we measured the height of each Clapper Rail nest, sampled vegetation at active Clapper Rail nests and at random locations, and measured the distance to the nearest tidally influenced body of water and the average height and density of vegetation. Early in the breeding season, the average nest height was lower at the Pascagoula (36 cm) than at Grand Bay (60 cm), but, as the season progressed, nest height increased at the Pascagoula only. Within both estuaries, Clapper Rail nest sites were more structurally complex than at random locations and were associated with a greater diversity of vegetation. Overall, daily survival rates of Clapper Rail nests were relatively high (0.97–0.99), with the majority of nest loss apparently the result of tidal flooding. Our results suggest that where diverse habitat was available, Clapper Rails varied the height of their nests as a mechanism to avoid nest loss from tidal flooding. Habitat alteration from factors such as sea-level rise and coastal development may lead to lower nest success because of a loss of diverse nesting habitat.