A strategy for incorporating uncertainty analysis techniques (sensitivity analysis, first order error analysis, and Monte Carlo simulation) into the mathematical water quality model QUAL2E is described. The model, named QUAL2E-UNCAS, automatically selects the input variables or parameters to be altered and stores and manipulates only the output of interest. The modeler is free to select the important output variables and locations in the stream network where information about uncertainty effects are desired. Applications of the model to the Withlacoochee River in Georgia and Florida demonstrate the importance of hydraulics, forcing functions and benthal phenomena.