It has been well known that it is not easy to quantify pollutant loads driven by non-point source pollution due to various factors affecting generation and transport mechanism of it. Especially pollutant loads through baseflow have been investigated by limited number of researchers. Thus in this study, the Web-based WAPLE (WHAT-Pollutant Load Estimation) system was developed and applied at study watersheds to quantify baseflow contribution of pollutant. In YbB watershed, baseflow contribution with WWTP discharge is responsible for 49.5% of total pollutant loads at the watershed. Among these, pollutant loads through baseflow (excluding any WWTP discharge) is responsible for 61.7% of it. In GbA watershed, it was found that 58.4% is contributed by baseflow with WWTP discharge 2.9% and 97.1% is by baseflow. For NbB watershed (without WWTP discharge), 52.3% of pollutant load is transported through baseflow. As shown in this study, it was found that over 50.0% of TN (Total Nitrogen) pollutant loads are contributed by non-direct runoff. Thus pollutant loads contributed by baseflow and WWTP discharge as well as direct runoff contribution should be quantified to develop and implement watershed-specific Best Management Practices during dry period.