Pecos assiminea (Assiminea pecos) is an endangered, little-known, cryptic microsnail occurring in moist karstic soil. Due to its small size and limited habitat preferences, research and population density estimates for this species have proven challenging. Here, we tested a range of survey methods and assessed their efficiency to capture microsnails and estimate their population density next to a sinkhole on Bitter Lake National Wildlife Refuge, Roswell, New Mexico, U.S.A. We used four different sampling methods: manual sifting and visual inspection of soil cores, light traps, beer traps, and Hester-Dendy plates. We also examined snail shells under different light wavelengths to test if they would become more visible, which they did not. We found most snails by sifting and visually inspecting the soil. Our estimations from manual sifting indicated that the population density of A. pecos is highest at around 3 m from the water's edge and 5–15 cm below the surface. Population density estimates at 3 m from shore were 6,200 snails per m². Furthermore, we found other snail species within our soil cores indicating that other microsnails utilize this habitat. Our method can aid studying A. pecos and other microsnails that live below the soil surface.