The small-clawed otter (Aonyx cinereus) is an IUCN vulnerable species that inhabits natural and rice-field landscapes of Southeast Asia. However, the habitat use of small-clawed otters in rice-field landscapes is largely unknown. Through a 53-week field survey and landscape analyses, we investigated latrine-site use by small-clawed otters in rice-field landscapes of West Sumatra, Indonesia. Using land-use and/or local environmental variables as predictors, we performed generalized linear model (GLM) analyses to explain the spatial patterns of latrine-site occurrence and otter visitation to latrine sites. Several latrine sites were used after more than 7 years from their initial discovery. Intermediate number of rice-field huts was the single most important predictor of latrine-site occurrence, while the distance to the nearest settlement, distance to the river, and mean water depth of the rice field adjacent to the latrine site were important predictors of otter visitation to latrine sites. These results indicate that the latrine-site preferences of small-clawed otters in rice-field landscapes most strongly associated with intermediate levels of rice farming activities. Because Indonesian rice fields are being degraded or disappearing at an accelerating rate, we emphasize the urgent need for the design and implementation of otter-friendly rice farming to conserve the small-clawed otter.