The Philadelphia Water Department (PWD) has recently developed a comprehensive Source Water Protection Program as part of its effort to improve Philadelphia's water environment. The program includes a source water assessment (SWA) partnership project, conducted in compliance with the Safe Drinking Water Act, for water suppliers in the Schuylkill and Delaware River Watersheds in Pennsylvania. These assessments include identification of over 5,000 potential sources of contamination over the entire watershed and intake-specific source prioritization at 50 intakes. To efficiently and cost-effectively develop such a large-scale source water assessment program (SWAP), a uniform and comprehensive prioritization process was established. This paper describes the data acquisition and development of an innovative data management system, the rainfall-runoff modeling process used to characterize the nonpoint sources, the advantages and disadvantages of the tools and tips for other such large source water protection initiatives. The contaminant inventory database management system incorporated both the point sources and the runoff contaminant loads. The sources were analyzed using selected criteria and prioritized for each of the drinking water intakes. This compilation of potential sources is one component of the SWAP process implemented for the two large-scale watersheds. The initial data compilation program relied heavily on downloads from several federal and state databases to quickly generate a list of over 5,000 wastewater, RCRA and other sources. The data was organized and verified using local water suppliers' data. Using a combination of geographic information system (GIS) processing and database management techniques, a comprehensive set of tools were developed to conduct preliminary screening of the sources for each intake and to generate input data files for EVAMIX, a multi-criteria prioritization model that was used in this project. The output from the model was compiled and processed using the database and GIS tools to develop the assessment reports for the various intakes. This paper explains the processes involved in the development of the database and GIS tools, provides guidance for other SWAP programs, and discusses the pitfalls to be avoided when using such large-scale watershed software tools. One of the critical elements of a SWAP program is the characterization of the nonpoint sources. The need to provide estimates of potential nonpoint source and runoff contaminant loads from a combined drainage area of over 11,000 square miles presented one of the more difficult challenges. The study area ranges from high density urbanized to agricultural areas. A comprehensive, basin-wide, long-term continuous simulation model of watershed hydrology and water quality loading met the challenge of modeling and quantifying contaminant loads. This paper describes the model methodology and its usefulness for such projects. Includes 2 references, figures.