We describe the development and potential applications of a new stream water quality model that can be operated in either steady or unsteady modes. The model predicts the seepage flow during the time when both the flow in the stream basin and the input waste loads are variable. It is applied to the case of wastewater discharge into the Salt River from the 91st Avenue wastewater treatment plant of Phoenix, Arizona. The model simulates variable flow discharge from the treatment plant and periodic drying of the clogging layer, which influence infiltration rates at the stream banks. The ultimate aim is to couple the flow model with a riparian vegetation model to predict the ecosystem response to unsteady, effluent-dominated stream dynamics. The model results will also be useful for resource managers to gain a better understanding of the dynamics of effluent-dominated systems. ¿ 1998 American Geophysical Union