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SWAT (Soil Water Assessment Tool) is a watershed mass-balance loading model. Recently equations from the water quality model QUAL2E have been incorporated into the SWAT model. QUAL2E is a steady-state model used to predict the concentration of in-stream parameters based on constant streamflow and inputs. The validity of the incorporation of the QUAL2E equations into SWAT has never been adequately confirmed. In order to test the validity of the water quality component of SWAT, two approaches were used. The first approached extracted the water quality subroutine from SWAT and emulated a steady-state simulation for comparison with QUAL2E output. The second approach utilized the entire SWAT program emulating a steady-state simulation for comparison with a comparable simulation in QUAL2E. The extracted subroutine steady-state simulations had a low standard error of prediction (0.071) compared to the QUAL2E output, with all of the calculated variables very similar at low concentrations. However, as initial concentrations increased the standard error also increased. The full SWAT model exhibited differences from the QUAL2E model in 2, 6 and 24 hour element retention time simulations. SWAT gave the same results regardless of retention time, with the differences between the output of the two models decreasing as the duration of retention time increased. The greatest discrepancies between the two models occurred in the DO and chlorophyll-a simulations. A minor change in the SWAT program, removing a default which made all retention times equal to one day, caused SWAT output in the 2 and 6 hour retention time simulations to better emulate the QUAL2E output. A limited test using modified algorithms for organic and dissolved phosphorus in the SWAT model was able to produce identical results to the QUAL2E simulation, leading to the conclusion that the QUAL2E equations may not have been correctly incorporated into the SWAT model. More analysis needs to be done to evaluate SWAT water quality algorithms.