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During periods of reduced precipitation, flow in low-order, upland streams may be reduced and may stop completely. Under these low flow conditions, fecal bacteria directly deposited in the stream dominate in-stream bacteria loads. When developing a Total Maximum Daily Load (TMDL) to address a bacterial impairment in an upland, rural watershed, direct deposit (DD) fecal bacteria sources (livestock and wildlife defecating directly in the stream) often drive the source-load reductions required to meet water quality criteria. Due to limitations in the application of existing watershed-scale water quality models, under low-flow conditions the models can predict unrealistically high in-stream fecal bacteria concentrations. This study used the Hydrological Simulation Program-FORTRAN (HSPF) to compare three low-flow DD simulation approaches and combinations (treatments) on two Virginia watersheds where bacterial impairment TMDLs had been previously developed and where low-flow conditions had been encountered. Results from the first watershed indicate that the Flow Stagnation (FS) method simulated significantly lower instantaneous water quality criterion violation rates at all allocation levels than the Control. The Stage Cut-off (SC) method reduced the livestock DD load compared to the Control, but produced significantly lower instantaneous criterion violation rates. The Surface Area (SA) method did not produce significantly different instantaneous criterion violation rates compared to the Control. Geometric mean criterion violation rates were not significantly different from the Control for any method. The distributions of maximum in-stream fecal coliform concentrations simulated by combining the methods SC + FS and SC + SA + FS were both significantly different from the Control. This research suggests that a combination of the SC and FS methods may be the most appropriate treatment for addressing unrealistically high in-stream bacteria concentrations simulated during low-flow conditions. However, this combination must be used with caution as the FS method may increase the maximum simulated in-stream fecal coliform concentration if HSPF simulates zero volume within the stream reach, as might happen during extended drought conditions.