Technical Abstract: Karst hydrology is characterized by multiple springs, sinkholes, and losing streams resulting from acidic water percolating through limestone. These features provide direct connections between surface water and groundwater and increase the risk of groundwater, spring and stream contamination. Anthropogenic activities (agriculture, tourism, urban and residential areas) accentuate the contamination potentials. The Soil and Water Assessment Tool (version 2005) was calibrated for the James River Basin, a large watershed (3,600 km2) in Southwest Missouri, to evaluate its ability to simulate flow and pollutant transport in karst areas. Losing streams were simulated by specifying high soil conductivities in the channels. The model was modified to allow infiltrations from sinkholes and losing streams to return to surface waters. The model was calibrated for flow, phosphorus and bacteria using data from four weather stations, five USGS flow gauges and four USGS water quality stations. Results indicated that flow calibration is satisfactory in the main stream reaches but needs to be improved in the upper reaches. Pollutant calibration was acceptable on a frequency basis only. Understanding the assumptions and the limitations is necessary to determine the future development needs of the SWAT model in this domain and to interpret the results obtained with the current version.