Studies of habitat selection can reveal important patterns to guide habitat restoration and management for species of conservation concern. Giant gartersnakes (Thamnophis gigas) are endemic to the Central Valley of California, where more than 90% of their historic wetland habitat has been converted to agricultural and other uses. Information about the selection of habitats by individual giant gartersnakes is needed to guide habitat restoration. We examined selection of microhabitats and vegetation types by adult female giant gartersnakes with radio telemetry at a site comprised of rice agriculture and restored wetlands using a paired case-control study design. Adult female giant gartersnakes were 15.6 (10.124.7) times more likely to be active (foraging, mating, or moving) when located in aquatic habitats than when located in terrestrial habitats. Microhabitats associated with cover, particularly emergent vegetation, terrestrial vegetation, and litter, were positively selected by giant gartersnakes. Individual giant gartersnakes varied greatly in their selection of rice and rock habitats, but little in their selection of open water. Tules (Schoenoplectus acutus) were the most strongly selected vegetation type, and duckweed (Lemna spp.), water-primrose (Ludwigia spp.), forbs, and grasses also were positively selected at the levels of availability observed at our study site. Management practices that promote the interface of water with emergent aquatic and herbaceous terrestrial vegetation will likely benefit giant gartersnakes. Restoration of native tule marshes will likely provide the greatest benefit to these threatened aquatic snakes.