John Clune is a Research Hydrologist who has worked at the Pennsylvania Water Science Center since 2007.
My core research is focused on understanding
- the environmental drivers and responses of nutrients and sediment in streams with an emphasis on the effectiveness of conservation practices, and
- the geochemistry of groundwater focusing on the quality of drinking water for the protection of public health.
Professional Experience
Adjunct professor for stream ecology at York College, Pennsylvania.
Provided research for the National Park Service (Grand Teton), US Army Corps of Engineers, University of Pittsburgh, Queens University Belfast, UTC Pratt and Whitney, and Lackawanna Conservation District.
Education and Certifications
Ph.D. Forest Resources, 2021, Penn State University
Dissertation: Toward Development of Nutrient Criteria for Streams of PennsylvaniaM.S. Biology, 2008, East Stroudsburg University
Thesis: Nutrient Supply Rates Relationships for Primary Production of Shallow Streams in the Mid-Atlantic StatesB.S. Civil Engineering, 2000, University of Pittsburgh
Science and Products
Pennsylvania and the Chesapeake Bay Watershed
Summarizing Science to Inform Management in the Chesapeake Bay Watershed
Science to Inform Management Priorities from Loads to Endpoints (SIMPLE)
Sediment Response of Stream Restoration Practices, Turtle Creek, Union County, Pennsylvania
USGS Chesapeake Publication Receives National Award for Superior Communication Product
Tracking Status and Trends in Seven Key Indicators of River and Stream Condition in the Chesapeake Bay Watershed
Susquehanna River and Basin
Greatest Opportunities for Future Nitrogen Reductions to the Chesapeake Bay Watershed are in Developed and Agricultural Areas
Regional Synthesis of Groundwater Quality in Domestic Supply Wells in Northeast and North Central Pennsylvania
Summarizing Scientific Findings for Common Stakeholder Questions to Inform Nutrient and Sediment Management Activities in the Chesapeake Bay Watershed
Water Quality Monitoring to Inform Conservation Management, Fishing Creek, Clinton County, Pennsylvania
Groundwater Quality of Domestic Supply Wells in Pennsylvania
Compilation of multi-agency water temperature observations for streams within the Chesapeake Bay watershed
Nitrogen sources to and export from the Chesapeake Bay watershed, 1950 to 2050
Compilation of data not available in the National Water Information System for domestic wells sampled by the U.S. Geological Survey in Clinton County, Pennsylvania, May-September 2017
Compilation of data not available in the National Water Information System for domestic wells sampled by the U.S. Geological Survey in Bradford County, Pennsylvania, May-August 2016
Tracking status and trends in seven key indicators of stream health in the Chesapeake Bay watershed
Nitrogen in the Chesapeake Bay watershed—A century of change, 1950–2050
Groundwater quality in relation to drinking water health standards and geochemical characteristics for 54 domestic wells in Clinton County, Pennsylvania, 2017
Drinking water health standards comparison and chemical analysis of groundwater for 72 domestic wells in Bradford County, Pennsylvania, 2016
Comparison of regression relations of bankfull discharge and channel geometry for the glaciated and nonglaciated settings of Pennsylvania and southern New York
Spatial and temporal variation of stream chemistry associated with contrasting geology and land-use patterns in the Chesapeake Bay watershed—Summary of results from Smith Creek, Virginia; Upper Chester River, Maryland; Conewago Creek, Pennsylvania; and Di
Sources of fine-grained sediment in the Linganore Creek watershed, Frederick and Carroll Counties, Maryland, 2008-10
Residence time, chemical and isotopic analysis of nitrate in the groundwater and surface water of a small agricultural watershed in the Coastal Plain, Bucks Branch, Sussex County, Delaware
Pesticides in ground water in selected agricultural land-use areas and hydrogeologic settings in Pennsylvania, 2003-07
Non-USGS Publications**
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Science and Products
- Science
Filter Total Items: 13
Pennsylvania and the Chesapeake Bay Watershed
USGS provides monitoring, analysis, modeling and research on streams and water quality to better understand the fate and transport of nutrients and sediment to the Susquehanna and other rivers, and their tributaries, and eventually to the Chesapeake Bay. Additional research focuses on emerging contaminants and other stressors that effect human and aquatic life in the watershed and estuary.Summarizing Science to Inform Management in the Chesapeake Bay Watershed
Stakeholders can use scientific insights to address their priority water-quality concerns. The USGS works with Chesapeake Bay stakeholders to identify and address priority questions that can help inform management decisions. These scientific insights can help guide nutrient and sediment management activities undertaken by Chesapeake Bay stakeholders. This webpage summarizes recent scientific...Science to Inform Management Priorities from Loads to Endpoints (SIMPLE)
Resource managers are working to improve water-quality in the Chesapeake to benefit the people who live in the region and the birds, fish, and other animals who rely on clean water in the watershed and the Bay. The U.S Geological Survey (USGS) supports resource managers and other Chesapeake stakeholders by providing science that informs restoration and conservation in the Chesapeake region. The...Sediment Response of Stream Restoration Practices, Turtle Creek, Union County, Pennsylvania
USGS is providing data and analyses to assess stream restoration effectiveness in Turtle Creek, Union County, Pennsylvania, by measuring differences in sediment erosion and deposition in restored and eroded stream reaches.USGS Chesapeake Publication Receives National Award for Superior Communication Product
The Award USGS received a 2022 Blue Pencil & Gold Screen Award, in the category of Technical/Statistical Reports, from the National Association of Government Communications (NAGC) for the U.S. Geological Survey Circular titled Nitrogen in the Chesapeake Bay Watershed—A Century of Change, 1950–2050. Each year the NAGC recognizes products that provide excellence in government communications and the...Tracking Status and Trends in Seven Key Indicators of River and Stream Condition in the Chesapeake Bay Watershed
Identifying and tracking the status of, and trends in, stream health within the Chesapeake Bay watershed is essential to understanding the past, present, and future trajectory of the watershed’s resources and ecological condition. A team of USGS ecosystem scientists is meeting this need with an initiative to track the status of, and trends in, key indicators of the health of non-tidal freshwater...Susquehanna River and Basin
In Pennsylvania, the USGS's water-resources roots date back to the late 1800's, with the initiation of streamflow gaging on the Susquehanna and Delaware Rivers and assessments of groundwater resources near Philadelphia. The USGS Pennsylvania Water Science Center continues to provide scientific information about the water resources of the Susquehanna River Basin, in cooperation with regional and...Greatest Opportunities for Future Nitrogen Reductions to the Chesapeake Bay Watershed are in Developed and Agricultural Areas
Issue: As human population has increased, land-use changes have led to increases in nutrients (nitrogen and phosphorus) and sediment into the Bay. The excess nutrients cause algal blooms which contribute to water-quality impairments such as low oxygen or hypoxia (dead zones), and poor water clarity in the Chesapeake Bay. Management efforts to improve water quality focus on dissolved oxygen needed...Regional Synthesis of Groundwater Quality in Domestic Supply Wells in Northeast and North Central Pennsylvania
USGS synthesized groundwater quality measurements in wells to characterize regional chemical characteristics of aquifers used for domestic supply in northeast and north central Pennsylvania.Summarizing Scientific Findings for Common Stakeholder Questions to Inform Nutrient and Sediment Management Activities in the Chesapeake Bay Watershed
Issue: The Chesapeake Bay Program (CBP) partnership is striving to improve water-quality conditions in the Bay by using a variety of management strategies to reduce nutrient and sediment loads. The partnership uses monitoring results and modeling tools to implement management strategies, relying on the scientific community to synthesize existing information and direct new research to address...Water Quality Monitoring to Inform Conservation Management, Fishing Creek, Clinton County, Pennsylvania
USGS conducted synoptic sampling of major-ion chemistry and the nitrogen and oxygen isotopic composition of nitrate in Fishing Creek during base flow to evaluate the occurrence and distribution of nutrients and to characterize biogeochemical processes.Groundwater Quality of Domestic Supply Wells in Pennsylvania
Most rural residents in Pennsylvania use groundwater from domestic supply wells for drinking, cleaning and other purposes. Some groundwater samples have been analyzed for private purposes, but those results generally are not readily available to the public. Many of the publicly available water-quality samples from rural areas were collected more than 30 years ago. Quality-assured groundwater... - Data
Compilation of multi-agency water temperature observations for streams within the Chesapeake Bay watershed
This data release collates stream water temperature observations across the Chesapeake Bay watershed from the USGS National Water Information System (NWIS), Water Quality Portal (WQP) and the USGS Aquarius (AQ) Time-Series database. Data retrieved from NWIS consists of aggregate (minimum, maximum and mean) daily values and continuous data from USGS monitoring stations. Values from the WQP containNitrogen sources to and export from the Chesapeake Bay watershed, 1950 to 2050
This U.S. Geological Survey data release contains datasets that combine past data with future projections of nitrogen sources and nitrogen export to the Chesapeake Bay watershed for the years 1950-2050. To help understand the effect of human and environmental changes over this time period, data for nitrogen sources from wastewater, agricultural fertilizer and manure, and atmospheric deposition areCompilation of data not available in the National Water Information System for domestic wells sampled by the U.S. Geological Survey in Clinton County, Pennsylvania, May-September 2017
This dataset contains the lithologic class and topographic position index information and quality-assurance and quality-control data not available in the online National Water Information System for 54 domestic wells sampled by the U.S. Geological Survey in Clinton County, Pennsylvania, May-September 2017. The topographic position index (TPI) for each well location was computed on the basis of a 2Compilation of data not available in the National Water Information System for domestic wells sampled by the U.S. Geological Survey in Bradford County, Pennsylvania, May-August 2016
This dataset contains the lithologic class and topographic position index information and quality-assurance and quality-control data not available in the online National Water Information System for 72 domestic wells sampled by the U.S. Geological Survey in Bradford County, Pennsylvania, May-August 2016. The topographic position index (TPI) for each well location was computed on the basis of a 25- - Multimedia
- Publications
Tracking status and trends in seven key indicators of stream health in the Chesapeake Bay watershed
“The Bay Connects us, the Bay reflects us” writes Tom Horton in the book “Turning the Tide—Saving the Chesapeake Bay”. The Chesapeake Bay watershed contains the largest estuary in the United States. The watershed stretches north to Cooperstown, New York, south to Lynchburg and Virginia Beach, Virginia, west to Pendleton County, West Virginia, and east to Seaford, Delaware, and Scranton, PennsylvanAuthorsSamuel H. Austin, Matt J. Cashman, John Clune, James E. Colgin, Rosemary M. Fanelli, Kevin P. Krause, Emily H. Majcher, Kelly O. Maloney, Chris A. Mason, Doug L. Moyer, Tammy M. ZimmermanByEcosystems Mission Area, Water Resources Mission Area, Environmental Health Program, Chesapeake Bay Activities, Eastern Ecological Science Center, Maryland-Delaware-D.C. Water Science Center, Pennsylvania Water Science Center, South Atlantic Water Science Center (SAWSC), Virginia and West Virginia Water Science CenterNitrogen in the Chesapeake Bay watershed—A century of change, 1950–2050
ForewordSustaining the quality of the Nation’s water resources and the health of our diverse ecosystems depends on the availability of sound water-resources data and information to develop effective, science-based policies. Effective management of water resources also brings more certainty and efficiency to important economic sectors. Taken together, these actions lead to immediate and long-term eAuthorsJohn W. Clune, Paul D. Capel, Matthew P. Miller, Douglas A. Burns, Andrew J. Sekellick, Peter R. Claggett, Richard H. Coupe, Rosemary M. Fanelli, Ana Maria Garcia, Jeff P. Raffensperger, Silvia Terziotti, Gopal Bhatt, Joel D. Blomquist, Kristina G. Hopkins, Jennifer L. Keisman, Lewis C. Linker, Gary W. Shenk, Richard A. Smith, Alex Soroka, James S. Webber, David M. Wolock, Qian ZhangGroundwater quality in relation to drinking water health standards and geochemical characteristics for 54 domestic wells in Clinton County, Pennsylvania, 2017
Despite the reliance on groundwater by approximately 2.4 million rural Pennsylvania residents, publicly available data to characterize the quality of private well water are limited. As part of a regional effort to characterize groundwater in rural areas of Pennsylvania, samples from 54 domestic wells in Clinton County were collected and analyzed in 2017. The samples were evaluated for a wide rangeAuthorsJohn Clune, Charles A. CravottaDrinking water health standards comparison and chemical analysis of groundwater for 72 domestic wells in Bradford County, Pennsylvania, 2016
Pennsylvania has the second highest number of residential wells of any state in the Nation with approximately 2.4 million residents that depend on groundwater for their domestic water supply. Despite the widespread reliance on groundwater in rural areas of the state, publicly available data to characterize the quality of private well water are limited. In Bradford County, more than half of the resAuthorsJohn Clune, Charles A. CravottaComparison of regression relations of bankfull discharge and channel geometry for the glaciated and nonglaciated settings of Pennsylvania and southern New York
Streambank erosion in areas of past glacial deposition has been shown to be a dominant source of sediment to streams. Water resource managers are faced with the challenge of developing long and short term (emergency) stream restoration efforts that rely on the most suitable channel geometry for project design. A geomorphic dataset of new (2016, n=5) and previous (1999–2006, n=96) estimates of bankAuthorsJohn Clune, Jeffrey J. Chaplin, Kirk E. WhiteSpatial and temporal variation of stream chemistry associated with contrasting geology and land-use patterns in the Chesapeake Bay watershed—Summary of results from Smith Creek, Virginia; Upper Chester River, Maryland; Conewago Creek, Pennsylvania; and Di
Despite widespread and ongoing implementation of conservation practices throughout the Chesapeake Bay watershed, water quality continues to be degraded by excess sediment and nutrient inputs. While the Chesapeake Bay Program has developed and maintains a large-scale and long-term monitoring network to detect improvements in water quality throughout the watershed, fewer resources have been allocateAuthorsKenneth E. Hyer, Judith M. Denver, Michael J. Langland, James S. Webber, J. K. Böhlke, W. Dean Hively, John W. CluneSources of fine-grained sediment in the Linganore Creek watershed, Frederick and Carroll Counties, Maryland, 2008-10
Sediment fingerprinting quantifies the delivery of fine-grained sediment from a watershed and sediment-budget measurements quantify the erosion and deposition of fine-grained sediment. Both approaches were used in the agricultural and forested 147-square-kilometer (km2) Linganore Creek watershed in Maryland from August 1, 2008 through December 31, 2010, to determine the sources of fine-grained (leAuthorsAllen C. Gellis, Gregory B. Noe, John W. Clune, Michael K. Myers, Cliff R. Hupp, Edward R. Schenk, Gregory E. SchwarzResidence time, chemical and isotopic analysis of nitrate in the groundwater and surface water of a small agricultural watershed in the Coastal Plain, Bucks Branch, Sussex County, Delaware
Nitrate is a common contaminant in groundwater and surface water throughout the Nation, and water-resource managers need more detailed small-scale watershed research to guide conservation efforts aimed at improving water quality. Concentrations of nitrate in Bucks Branch are among the highest in the state of Delaware and a scientific investigation was performed to provide water-quality informationAuthorsJohn W. Clune, Judith M. DenverPesticides in ground water in selected agricultural land-use areas and hydrogeologic settings in Pennsylvania, 2003-07
This report was prepared by the U.S. Geological Survey (USGS) in cooperation with the Pennsylvania Department of Agriculture (PDA) as part of the Pennsylvania Pesticides and Ground Water Strategy (PPGWS). Monitoring data and extensive quality-assurance data on the occurrence of pesticides in ground water during 2003–07 are presented and evaluated; decreases in the land area used for agriculture anAuthorsConnie A. Loper, Kevin J. Breen, Tammy Zimmerman, John W. CluneNon-USGS Publications**
Clune, J.W., 2021, Toward the Development of Nutrient Criteria for Streams of Pennsylvania, Doctoral dissertation, Penn State University
Clune, J.W., Crawford, J.K., and Boyer, E.W., 2020, Nitrogen and Phosphorus Concentration Thresholds toward Establishing Water Quality Criteria for Pennsylvania, USA: Water, v. 12, no. 12, p. 3550.
Clune, J.W., Crawford, J.K., Chappell, W.T., and Boyer, E.W., 2020, Differential effects of land use on nutrient concentrations in streams of Pennsylvania: Environmental Research Communications, v. 2, no. 11, p. 115003.
Denver, J.M., Ator, S.A., Lang, M.W., Fisher, T.R., Gustafson, A.B., Fox, R., Clune, J.W. and McCarty, G.W., 2014, Nitrogen fate and transport through palustrine depressional wetlands along an alteration gradient in an agricultural landscape, Upper Choptank Watershed, Maryland: Journal of Soil and Water Conservation vol. 69, p 1-16, doi:10.2489/jswc.69.1.1.Clune, J.W., Gellis, A.C., and McKee, L.G. 2010. Agricultural Soil Erosion Rates for the Linganore Creek Watershed in the Piedmont Physiographic Province of the Chesapeake Bay Watershed: 2nd Joint Federal Interagency Proceedings, Las Vegas, NV, June 27 – July 1, 2010.**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.