The marsh rice rat (Oryzomys palustris) is a semiaquatic rodent occurring in wetland habitats throughout the southeastern United States and along the Atlantic Coast. A lack of understanding of its ecology and distribution in inland parts of its range limits our ability to assess the species' status and needs. We trapped rice rats at random and previously occupied, wetland-dominated sites in 5 southern Illinois watersheds during 2007–2009 to determine key variables affecting habitat occupancy by the species. We detected rice rats within 3 of 5 watersheds, 16 of 48 sites, and at 5 new locations. Most rice rats were captured in permanent or semipermanent emergent wetlands (n  =  89; 46.3% of total captures) or roadside ditches in wetland patches (n  =  73; 38.0%). Habitat associations determined using logistic regression and occupancy modeling provided similar results. Percent herbaceous cover and percent visual obstruction (0.0–0.5 m) were the most important microhabitat variables positively influencing rice rat occurrence. In areas surrounding wetlands, the proportion composed of upland grass was the best predictive variable of rice rat occurrence among landcover models. Estimates of daily detection probability were high (0.44–0.87). The likelihood of occupancy increased with the proportion of upland grass cover adjacent to wetland complex and percent herbaceous cover at the microhabitat scale. Inland metapopulations of rice rats are clustered throughout the southeastern United States in appropriate wetland complexes. Construction, restoration, and protection of emergent wetlands, and consideration of connectivity and adjacent grasslands, should benefit rice rat populations.