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Dynamic modeling and probabilistic analysis techniques were used to analyze water quality impacts and to calculate proposed NPDES discharge permit limits for the discharge of secondary treated wastewater from the Sacramento Regional Wastewater Treatment Plant (SRWTP) to the Sacramento River near Freeport, CA. Because of the unique configuration of this discharge, standard models cannot be used describe dilution within the effluent plume downstream of the discharge, and standard methods of calculating effluent limits are inapplicable. Dynamic modeling was used to predict dilution within the plume downstream of the SRWTP diffuser over a 70-year hydrologic period, and a linked probabilistic analysis was used to evaluate water quality constituent concentrations and compliance with relevant water quality criteria. Extensive field studies have been conducted to calibrate and verify models (Fischer Delta Model) and to verify model results (FLOWMOD) used in these analyses. Dynamic modeling and probabilistic analysis techniques, when supported and verified by field data, offer a new and more accurate approach to evaluating water quality impacts and calculating effluent limits.