Clean fresh water is becoming an increasingly critical resource that will become evermore precious as more societies industrialize and population pressure increases. The critical nature of the water resource expands the vulnerability of the water supply to political and terrorist activities. With this expanded vulnerability, the importance of forensic analysis in management of water resources and protection from contamination increases. Herein, we propose monitoring the accelerated generation of drinking water microbial biofilms on "traps." The major problem with protecting water is the great dilution of the potential pathogens and toxicants. Our solution to this monitoring problem is to utilize the propensity of microbes and toxicants to concentrate at surfaces in biofilms. A logical, cost-effective method to sample pathogenic microbes and membrane-active toxicants in water is to recover biofilms from strategically placed surfaces. Modeling of the total system to maximize protection of each water system component would help identify the location of specific instrumented nodes. Nodes would be outfitted with sensors for reporting rates of general biofilm formation and some specific biofilm components. A change in biofilm at a node, or at some interval period, would signal recovery of some previously placed and colonized bio-trap beads at that node, which would then be rapidly extracted and examined for pathogen lipid, DNA biomarkers, and toxicants by tandem mass spectrometry. The lipid extraction facilitates recovery of DNA that can be used for specific microbial and virus identification. The biomarker analysis enables a much faster and comprehensive analysis than the classic microbial isolation and culture techniques currently used to protect the water supply. The total watershed collection, treatment, and distribution system would be instrumented to provide comprehensive monitoring for threat with time for purification and interdiction systems to protect the drinking water supply in the distribution system.