In the United States, pathogens are the leading cause for rivers and streams to exceed water quality standards. The Spatially Explicit Load Enrichment Calculation Tool (SELECT) was developed to estimate bacterially contaminated water bodies based on spatial factors such as land use, soil, and population density. SELECT was originally automated using Visual Basics for Applications (VBA), which is no longer supported by the current version of ArcGIS. The aim of this research was to develop a new SELECT interface, pySELECT, using the Python programming language and to incorporate a rainfall-runoff E. coli transport module to simulate E. coli loads resulting from urban sources, such as dogs and on-site wastewater treatment systems. The pySELECT tool was applied to Lavon Lake, a semi urban study watershed in Northeast Texas. The highest potential E. coli loads were in the areas closest to the Dallas-Fort Worth metroplex, and the highest transported loads were located downstream from those identified hotspots or where the most runoff was generated. Watershed managers can use pySELECT to develop best management practices on the specific areas and fecal sources that contribute fecal contamination into a waterbody.