Scientific uncertainty inherent in the development of Total Maximum Daily Load (TMDL) standards for non-point source pollutants such as sediment hampers the program’s effectiveness. Sediment is an important water quality parameter because deposition in streams and lakes adversely affects aquatic ecosystems. Equally important, suspended sediment is a transport mechanism for nutrients, pesticides and pathogens. This paper presents an alternative methodology that permits statistically valid calculation of sediment TMDL uncertainty. The sediment delivery computer simulation technology used for this project, the Geo-spatial interface for the Water Erosion Prediction Project (GeoWEPP), is capable of simulating single storm events and provides daily output useful for TMDL statistical analysis.