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The Soil and Water Assessment Tool (SWAT) model is recognized as one of the top hydrological models applied for addressing hydrologic and environmental issues. This is the first review on the SWAT model studies in Southeast Asia, with an emphasis on its applications, current challenges and future research directions. A total of 126 articles were identified since 2006; roughly 50% of these studies were conducted in Vietnam or Thailand. About 16% of the studies were performed at a transnational scale, which included Cambodia, Lao PDR, Thailand, and Vietnam. Model capability assessment, land use, and climate change assessment are the main SWAT applications that have been reported for the region. Most of the SWAT calibration and validation results for these studies were classified as satisfactory to very good results based on widely recognized performance indicators. However, the parameterization, calibration and validation procedures are not well reported in some articles. Availability of reliable data is one of the main problems that SWAT users are confronted with, as these data are either not freely available or restricted from public access in some countries. Hence, future studies should be considered on identification and development of reliable input data for SWAT modeling. SWAT model modification based on the SEA climate, geographical and land use conditions is another research direction to be considered in the future. Moreover, application of SWAT for extreme events simulation requires more attention in this region.