In recent years, there has been demand for precise estimations of pollutant loads on nationwide scale for the development of appropriate site specific (watershed specific) policies to reduce the negative impact of pollutant loads. River flow data and water quality data that were previously collected by various research institutes and universities for specific research purposes for a limited period was utilized in this study. However, only TMDL 8-day interval flow and water quality data were available in national scale. Three watersheds were selected and pollutant loads were calculated by two methods i.e., Numeric Integration (NI) method and Soil and Water Assessment Tool (SWAT). Subsequently, the results were compared to determine the appropriate method for monitoring nonpoint source networks nationwide. The SWAT model was calibrated and its estimated daily flow data were used in the NI method with estimated sediment data for 8-day monitoring data for three watersheds. The results indicated that the quantity of pollutant loads estimated with the NI and SWAT are different to some degrees especially during the summer season for all the three study watersheds. Thus, more frequent sampling of water quality is needed for nonpoint source pollutant estimation.