The extent of nonpoint source pollution (NPSP) generated from upstream catchment areas of a reservoir is normally estimated based on a design rainfall. However, rainfall generally varies in different seasons. This seasonal change may significantly influence the estimation of runoff volume and associated NPSP arising within a reservoir watershed. The NPSP management, reservoir operation, and water treatment operation strategies developed based on the estimation will also be altered. This study analyzes the effects of monthly and seasonal variation in precipitation on the estimation of pollution levels from non-point sources in a reservoir watershed. The area studied is the Derchi reservoir watershed located in central Taiwan. This watershed is subdivided into twenty-six sub-watersheds, and the Thiessen method is used to determine the rainfall intensity in each sub-watershed. Runoff pattern and NPSP contributions for each sub-watershed are estimated using the AGNPS model. Results show significant seasonal variation in precipitation; estimated NPSP loads likewise vary significantly over time. Seven- to one hundred-fold differences among monthly and seasonal estimations of phosphorus and sediment loads are observed.