Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment. W aterborne pathogens pose a health risk to recreational water users (1), in drinking water systems (2), and in aquatic organisms such as shellfish that are consumed by humans (3). These waterborne pathogens include more than 40 different groups or genera, including viruses, bacteria, protozoa, cyanobacteria, and helminths (4). Additional waterborne pathogens will doubtless emerge over time due to increased proportions of sensitive populations, globalization of commerce, microbial evolution, and use of reclaimed water as drinking water (5). Many waterborne pathogens originate from fecal pollution in storm water runoff from agricultural and urban surfaces (6) or direct release of untreated sewage to surface water (7). Additional sources of waterborne fecal pathogens include wildlife and domesticated animals such as deer, dogs, raccoons, cats, and wild avian species (8). Still other waterborne pathogens, such as Vibrio spp., are autochthonous to aquatic environments (9).The microbiological safety of surface water has been assessed for over a century by enumeration of fecal indicator bacteria (FIB) (10). Other monitoring techniques such as microbial source tracking (MST) are advantageous compared to enumeration ...