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When developing a bacterial impairment Total Maximum Daily Load (TMDL) in an upland rural watershed, in-stream direct deposition of livestock and wildlife feces is a significant bacteria source. Direct deposition (DD) is often the main bacteria source driving the reductions needed to meet water quality standards. During dry weather conditions, when DD may be the only bacteria source, low-order upland streams frequently stop flowing. However, due to limitations in water quality simulation methods, the models continue to predict flow when, in fact, either no flow or only discontinuous flow is occurring. During these low flow conditions, even small amounts of bacteria deposited directly in the stream result in predicted bacteria concentrations much higher than what would realistically occur. These erroneously high simulated in-stream bacteria concentrations are translated into the TMDL in the form of bacteria-source load reductions that are much more severe than what may be actually needed to improve water quality.