Small mammals support the ecological integrity of wetlands, and data on their diversity, richness, abundance, habitat use, and anthropogenic threats are essential for conservation management of wetland ecosystems. We assessed four different habitat types (forest, agriculture farm, grassland, and riparian) in Gantey-Phobji Ramsar site, Bhutan. We used Sherman and pitfall traps to capture and recapture animals, and we confirmed species based on morphometric measurements. We recorded environmental variables and anthropogenic activities that might alter small mammal presence, abundance, and diversity. We recorded 7 species and 128 individuals, as new record for the Ramsar site. Agricultural land has the highest species richness, and the forest had the highest diversity of small mammals. Small mammals used agricultural land as macrohabitat and shrubs as microhabitat. Small mammal occurrence varied in each habitat we sampled; therefore, holistic conservation interventions specific to habitat type are essential to conserve both wetlands and small mammals.