The availability of potable water is essential to protect the health of soldiers in combat and training. Current methods for the detection of pathogens or their indicator organisms typically require at least 24 hours, and perhaps as much as several days. Recent and ongoing advances in gene amplification and related measurement technologies offer the promise of developing a system that can be used to characterize these pathogens or their indicators in a fraction of the time now required. The Phase I project results have demonstrated the feasibility elements leading to the implementation of a prototype field portable system. These elements included a filtering system to isolate the E. coli bacteria from lake water samples, demonstration of a more efficient microwave lysis capability, and the evaluation, optimization and implementation of the E. coli DNA amplification process. In the proposed Phase II project, we plan to develop further the system components leading to the implementation of a prototype portable water analysis system. These components include an improved filtering system and survey of water sample types, optimization of the microwave lysis and DNA amplification efficiencies, and a simplified detection system for the amplification products.