Standard methods to identify microbial contaminants in the environment are slow, laborious, and can require specialized expertise. This study investigated electrochemical detection of microbial contaminants using commercially available, hand-held instruments. Electrochemical assays were developed for a red tide dinoflagellate (Karenia brevis), fecal-indicating bacteria (Enterococcus spp.), markers indicative of human sources of fecal pollution (human cluster Bacteroides and the esp gene of Enterococcus faecium), bacterial pathogens (Escherichia coli 0157:H7, Salmonella spp., Campylobacter jejuni, Staphylococcus aureus), and a viral pathogen (adenovirus). For K. brevis, two assay formats (Rapid PCR-Detect and Hybrid PCR-Detect) were tested and both provided detection limits of 10 genome equivalents for DNA isolated from K. brevis culture and amplified by PCR. Sensitivity with coastal water samples was sufficient to detect K. brevis that was "present" (<or=1000 cells/l) without yielding false positive results and the electrochemical signal was significantly different than for samples containing cells at "medium" concentrations (100,000 to<10(6)cells/l). Detection of K. brevis RNA was also shown. Multi-target capability was demonstrated with an 8-plex assay for bacterial and viral targets using isolated DNA, natural beach water spiked with human feces, and water and sediments collected from New Orleans, Louisiana following Hurricane Katrina. Furthermore, direct detection of dinoflagellate and bacterial DNA was achieved using lysed cells rather than extracted nucleic acids, allowing streamlining of the process. The methods presented can be used to rapidly (3-5h) screen environmental water samples for the presence of microbial contaminants and have the potential to be integrated into semi-automated detection platforms.