The habitat use and movements of the round stingray Urobatis halleri were compared between shallow restored and natural habitats of the Anaheim Bay Estuary (CA, U.S.A.) in relation to water temperature. Restored habitat remained significantly warmer than natural habitat from spring through to autumn. Strong sexual segregation occurred in the restored habitat with mature female U. halleri forming large unisex aggregations in summer, during months of peak seasonal water temperatures, and males only present during spring. Most mature females collected from restored habitat during months of high abundance were determined to be pregnant using non-invasive field ultrasonography. Tagged females typically spent <14 days in the restored habitat, using the habitat less as seasonal water temperatures decreased. Females tended to emigrate from the estuary by mid-August, coinciding with the time of year for parturition. The elevated water temperatures of the restored habitat may confer an energetic cost to male U. halleri, but females (particularly pregnant females) may derive a thermal reproductive benefit by using warm, shallow habitats for short periods of time during months of peak water temperatures. These findings have management implications for the design of coastal habitat restoration projects and marine protected areas that incorporate thermal environments preferred by aggregating female elasmobranchs.