When developing a Watershed Protection Plan (WPP) or a Total Maximum Daily Load (TMDL), it is often difficult to accurately assess the pollutant load for a watershed because insufficient water quality monitoring data are available. According to the Texas Commission on Environmental Quality (TCEQ), there are 274 bacteria impairments in Texas water bodies out of a total of 386 impaired water bodies. Bacteria concentrations are often more sparse than other types of water quality data which hinders the development of WPPs or TMDLs. The Spatially Explicit Load Enrichment Calculation Tool (SELECT) was used to develop WPPs for three rural watersheds in Texas that are impaired due to E. coli bacteria. SELECT is an automated Geographical Information System (GIS) tool that can assess pathogen loads in watersheds using spatial factors such as land use, population density, and soil type. WPPs were developed for three rural Texas watersheds: Buck Creek, Lampasas River, and five sub-watersheds of the Little Brazos River. The results show how SELECT methodology was applied to each watershed and adapted based on stakeholder concerns and data availability. The highest potential contributors were identified as cattle across all three watersheds and areas of concern were highlighted to more effectively apply best management practices (BMPs).