The Soil and Water Assessment Tool (SWAT) ecohydrological model was utilized to simulate fecal contamination in the 1937 km2 Selangor River Watershed in Malaysia. The watershed conditions posed considerable challenges owing to data scarcity and tropical climate conditions, which are very different from the original conditions that SWAT was developed and tested for. Insufficient data were compensated by publicly available data (e.g., land cover, soil, and weather) to run SWAT. In addition, field monitoring and interviews clarified representative situations of pollution sources and loads, which were used as input for the model. Model parameters determined by empirical analyses in the USA (e.g., surface runoff, evapotranspiration, and temperature adjustment for bacteria die-off) are thoroughly discussed. In particular, due consideration was given to tropical climate characteristics such as intense rainfall, high potential evapotranspiration, and high temperatures throughout the year. As a result, the developed SWAT successfully simulated fecal contamination ranging several orders of magnitude along with its spatial distribution (i.e., Nash-Sutcliffe Efficiency (NSE) = 0.64, Root Mean Square Error-Observations Standard Deviation Ratio (RSR) = 0.64 at six mainstem sites, and NSE = 0.67 and RSR = 0.57 at 12 major tributaries). Moreover, mitigation countermeasures for future worsening of fecal contamination (i.e., E.coli concentration > 20,000 CFU/100 mL for 690 days during nine years at a raw water intake point for Kuala Lumpur [KL] residents) were analyzed through scenario simulations, thereby contributing to discussing effective watershed management. The results propose improving decentralized sewage treatment systems and treating chicken manure with effective microorganisms in order to guarantee water safety for KL residents (i.e., E.coli concentrations <20,000 CFU/100 mL throughout the period, considering Malaysian standards). Accordingly, this study verified the applicability of SWAT to simulate fecal contamination in areas that are difficult to model and suggests solutions for watershed management based on quantitative evidence.