Using Microbial Source Tracking To Identify Fecal Contamination Sources in Lake Montauk on Long Island, New York

Scientific Investigations Report 2022-5038
Prepared in cooperation with Concerned Citizens of Montauk and New York State Department of Environmental Conservation
By: , and 



The U.S. Geological Survey worked in cooperation with the Concerned Citizens of Montauk and the New York State Department of Environmental Conservation to assess the potential sources of fecal contamination entering Lake Montauk, an artificial embayment on the tip of the southern fork of Suffolk County, Long Island, New York. Water samples are routinely collected by the New York State Department of Environmental Conservation in the harbor and analyzed for fecal coliform bacteria, an indicator of fecal contamination, to determine the need for closure of shellfish beds for harvest and consumption. Fecal coliform and other bacteria are an indicator of the potential presence of pathogenic (disease-causing) bacteria. However, indicator bacteria alone cannot determine the biological or geographical sources of contamination; therefore, microbial source tracking was implemented to determine various biological sources of contamination. In addition, information such as the location, weather and season, and surrounding land use where a sample was collected help determine the geographical source and conveyance of land-based water to the embayment.

Overall, human and waterfowl markers were infrequently and sporadically present in source and receptor samples at low concentrations. By evaluating the microbial source tracking markers alongside fecal coliform data and land-use information, geographical sources of fecal contamination discharging from various source sites, such as culverts and ponds, were better differentiated. Analysis revealed that stormwater runoff and pond drainage were the most likely transport mechanisms for fecal contamination to Lake Montauk. When considering Lake Montauk as a whole, the highest frequency of fecal coliform detections in source site samples was found to be under wet summer conditions, as evidenced by the high fecal coliform concentrations at the South Beach, Stepping Stones Pond, and Stepping Stones Pond Culvert sites (300, 220, and more than 16,000 most probable number per 100 milliliters, respectively). No point sources of fecal coliform contamination to Lake Montauk were identified; however, receptor site samples adjacent to marinas (Lake Montauk Inlet and Star Island North sites) had a high frequency of human marker detections but were associated with fecal coliform concentrations at or below the reporting limit. The absence of fecal coliform and human microbial source tracking markers in groundwater samples indicated that water from septic systems did not influence the lake during this study. Further, the sandy sediment sample collected at the South Beach site was negative for all microbial source tracking markers and is unlikely to contribute fecal coliform from the tested host organisms when resuspended in the water column through tidal shifts or boat activity.

Suggested Citation

Tagliaferri, T.N., Fisher, S.C., Kephart, C.M., Cheung, N., Reed, A.P., and Welk, R.J., 2022, Using microbial source tracking to identify fecal contamination sources in Lake Montauk on Long Island, New York: U.S. Geological Survey Scientific Investigations Report 2022–5038, 16 p.,

ISSN: 2328-0328 (online)

Study Area

Table of Contents

  • Acknowledgments
  • Executive Summary
  • Introduction
  • Site Description
  • Approach and Methods
  • Results
  • Classification of Source Sites
  • Summary
  • References Cited
  • Appendix 1. Sample Collection in Lake Montauk on Long Island, New York
Publication type Report
Publication Subtype USGS Numbered Series
Title Using microbial source tracking to identify fecal contamination sources in Lake Montauk on Long Island, New York
Series title Scientific Investigations Report
Series number 2022-5038
DOI 10.3133/sir20225038
Year Published 2022
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) New York Water Science Center
Description Report: vi, 16 p.; Database
Country United States
State New York
Other Geospatial Lake Montauk
Online Only (Y/N) Y
Additional Online Files (Y/N) N
Google Analytic Metrics Metrics page
Additional publication details