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National Point Source Discharge Elimination System (NPDES) permits, by state environmental regulatory agencies, are used to control point source pollution in a watershed. Controlling point source pollution through NPDES permitting has resulted in significant improvements in stream and lake water quality. Most often these permits require point source dischargers to discharge pollutants at a fixed rate and continuously monitor their discharges to demonstrate that they are in compliance with the permit. Since point source dischargers discharge at a fixed rate, during low flow periods, water quality impairments often result from point source discharges. On the contrary, during high flow periods contributions from point source dischargers are very small. In addition, stream flows are also affected by inter-annual climate variability resulting from a number of ocean-atmosphere phenomena that operate at seasonal to decadal time scales. In the Southeast, climate variability predominantly results from one such phenomenon called El Nio Southern Oscillation (ENSO). Currently, reliable ENSO forecasts are being issued by National Oceanic and Atmospheric Administration (NOAA) that can be used in the NPDES permitting process. In this paper, we first quantify the effect of point source discharge on seasonal and inter-annual phosphorus loading in a saugahatchee watershed in Alabama using the Soil and Water Assessment Tool (SWAT), and then demonstrate how ENSO forecasts can be used in the NPDES permitting process. The SWAT model was calibrated and validated for flow, sediment, and total phosphorus. The model was then used to demonstrate how ENSO can be incorporated in the NPDES permit.