Microbial Source Tracking in the Lower Passaic River Basin Study Area, New Jersey

Microbial Source Tracking in Second and Third Rivers, New Jersey

The USGS New Jersey Water Science Center is partnering with the Passaic Valley Sewerage Commission (PVSC) on an Urban Waters Federal Partnership project in the Lower Passaic Study area.  The objective of the project is to investigate the occurrence and potential sources of E. coli fecal indicator bacteria in the urbanized Second River and Third River tributaries to the Passaic River. The tributaries do not have any permitted point source discharges, however high levels of microbial contamination have been found in the waterbodies. This project supports efforts by PVSC, the U.S. Environmental Protection Agency and other partners to identify potential sources of pathogens and remediate sources of microbial contamination in the Second River and Third River basins. The project will provide further information on the spatial and temporal distribution of bacterial contamination and potential pathogen sources.

Samples will be collected from eight stream sites; four sites on the Second River and four sites on the Third River at baseflow and runoff conditions during 10 sampling events. Measurements of water temperature, specific conductance, pH, dissolved oxygen, and turbidity will be collected in the field. Water samples will be analyzed for E. coli, caffeine, and specific biomarkers (human, dog , bird and deer). Data from this project will be used to evaluate the impacts of nonpoint source runoff on instream pathogens.

Microbial Source Tracking in Molly Ann Brook, New Jersey

The U.S. Geological Survey, in partnership with the Passaic Valley Sewerage Commission, EPA Region 2, and the Lower Passaic River Urban Waters Federal Partnership, is conducting a comprehensive investigation into fecal contamination within Molly Ann Brook, a highly urbanized tributary of the Lower Passaic River. While previous studies have identified widespread fecal indicator bacteria (FIB) issues throughout the Passaic River basin, little has been known about specific sources within the Molly Ann Brook watershed. Historical data show that levels of E. coli consistently exceed New Jersey surface-water quality standards, even during dry weather, indicating multiple ongoing contamination inputs from human, wildlife, and domestic animal sources.

 This project uses both traditional E. coli monitoring and advanced microbial source tracking (MST) methods to pinpoint where contamination originates. Sampling during both wet- and dry‑weather conditions, combined with innovative tools such as the Fluidion in‑situ rapid bacteria analyzer, will provide a detailed picture of when and where fecal contamination enters the brook. The results will help federal, state, and local partners identify problem areas, guide remediation efforts, and support long‑term goals for cleaner, safer, and more accessible waterways throughout the Lower Passaic River system. 

For information about other USGS Urban Waters Federal Partnership Cooperative Matching Funds projects please visit

Urban Waters Federal Partnership Cooperative Matching Funds Projects  

For more information on studies in the lower Passaic River basin, please visit

The EPA Urban Waters Lower Passaic Urban Waters Partnership

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USGS Research Team:

Kat Calahane (Project Chief)

Dan Skulski