Tropical rice fields with asynchronous growth stages provide a good model to investigate the effects of landscape heterogeneity on the use of agricultural landscapes by wildlife. The small-clawed otter (Aonyx cinereus) uses rice fields as latrine sites in Southeast Asia. Through a 53-week survey of latrine sites, we analyzed the spatiotemporal patterns of latrine-site use by small-clawed otters in an asynchronous rice field in West Sumatra, Indonesia. Based on a generalized linear mixed model incorporating local environmental factors, otter latrine-site visitation was positively associated with the vegetative stage of rice cultivation and the biomass of a major prey item, the golden apple snail (Pomacea canaliculata). The vegetative stage of rice cultivation and golden apple snail biomass were closely associated with deep water in rice fields; therefore, water availability in rice fields is likely important in determining the spatiotemporal patterns of small-clawed otter latrine-site use in the asynchronous rice field landscape. To consistently provide latrine sites for small-clawed otters, we recommend that asynchronous rice cultivation be maintained, or zoning of synchronous and asynchronous rice cultivation areas be planned in the region.