Identification of habitat variables that are associated with patch occupancy can provide a solid foundation for conservation, especially when habitats and landscapes are affected by human activities. As a case study to investigate the importance of landscape complementation and habitat quality for conservation, we examined the habitat preferences of a vulnerable native rodent, the false water rat (Xeromys myoides Thomas). In this study, results from surveys for animal presence and recording of habitat attributes in localities in south-east Queensland showed that X. myoides prefers a habitat with a wide mangrove zone of short mangroves and a high percentage of relatively tall vegetation cover in the sedge/saltmarsh zone. The absence of X. myoides from areas of likely habitat at a large scale can be attributed, at least in part, to the local habitat variables that overrode predictions based at a large scale. The findings suggest that availability of suitable habitat is a factor limiting the distribution and abundance of X. myoides. It is clear that landscape complementation influences patch occupancy and should be an essential consideration for conservation programs.