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A TMDL was developed for the Shoal Creek Watershed, a 365-km2 watershed in southwest Missouri. The watershed consists of grazed or hayed pastures (89%) fertilized with poultry litter and commercial nitrogen and some wooded areas (11%). The cattle roam freely through the pastures year-round and we estimated that 25% of the pastures have direct access to the stream. Potential sources of bacterial contamination were determined through DNA source tracking technologies. The technology was used to quantify the bacteria contribution from poultry litter spread on pastures, grazing cattle, wildlife, failing septic systems, and direct inputs such as cattle standing in the streams or pipes discharging wastewater into the streams.

The Soil and Water Assessment Tool was used to simulate the flows in Shoal Creek as well as the fate and transport of nutrients in the watershed. The model was calibrated and validated using 3 years of daily flow data and 18 months of weekly nutrient data. The new bacteria equations in SWAT were then tested on this watershed. They include decay processes of bacteria in the streams as well as on the land and in the soil. The decay rates in soil water, in the soil, and in stream water are allowed to vary with water and air temperature. These equations were tested with 18 months of weekly fecal E. coli concentrations collected from grab samples. The model was used to develop and simulate alternative management practices that comply with the water quality criteria required for recreational uses of this stream.