National Research Program

Hydrologic, Ecological, and Biogeochemical Processes in Flowing Waters

There is increasing recognition that the ecological function of rivers, streams, and wetlands are inseparable from the physics of flowing water and its interactions with the aquatic, terrestrial, and subsurface components that delineate the “river and wetland corridor”.  It is the interplay between ecological, geomorphic, hydrologic, and biogeochemical processes that determines ecosystem function.  These factors strongly influence how water quality and quality of aquatic and riparian habitat respond to human disturbances and changing climate.  Improved conservation and restoration of river and wetland corridors requires an integrated approach that recognizes 1) linkages between surface and subsurface flows moving through terrestrial, riparian and aquatic components, and 2) feedbacks between flowing water and the geomorphic and ecological components that together modulate fluid flow, roughness, sediment entrainment and channel morphology in ways that further affect mass transfer of solutes and sediments between zones with different capacities for biogeochemical reactions.  Many of the critical hydrologic and biogeochemical processes occur in complex aquatic environments at close proximity to the sediment interface, within periphyton layers, and on leaves of aquatic and emergent plants where processes are hidden from detection by standard sampling protocols.  Our project addresses the profound need for new concepts, field methods, and cross-disciplinary models to address both the fundamental processes and their cumulative effects on basin-scale water quality and habitat value.

Our project follows four main lines of investigation: (1) developing new concepts and tools to detect and quantify hydrologic fluxes, biogeochemical transformations, and interactions with ecological components within flowing surface waters, including highly episodic flows across floodplains and difficult to detect subsurface flows through hyporheic flow paths beneath stream channels, (2) estimating cumulative effects of those processes at larger (stream-reach and drainage basin) scales using natural and introduced tracers as well as improved and increasingly available data sets from airborne and satellite remote sensing to help integrate across the small-scale variability, (3) improving and advancing the use of numerical modeling codes for analyzing coupled terrestrial and aquatic ecological processes with surface and subsurface flow and transport phenomena, and 4) synthesizing a national-scale understanding of transport conditions in river and wetland corridors across gradients in climate, surficial geology, and human disturbance in the United States that influence residence time of water and fate of dissolved and fine particulate materials in the nation’s flowing waters. For additional information about this project, see project home page.


Harvey, J.W., Noe, G.B., Larsen, L.G., Nowacki, D.J., and McPhillips, L.E., 2011, Field flume reveals aquatic vegetation's role in sediment and particulate phosphorus transport in a shallow aquatic ecosystem: Geomorphology, v. 126, no. 3-4, p. 297-313. doi:10.1016/j.geomorph.2010.03.028 (on-line abstract of journal article)

Larsen, L.G., and Harvey, J.W., 2011, Modeling of hydroecological feedbacks predicts distinct classes of landscape pattern, process, and restoration potential in shallow aquatic ecosystems: Geomorphology, v. 126, no. 3-4, p. 279-296. (on-line abstract of journal article)

Larsen, L., Aumen, N., Bernhardt, C., Engel, V., Givnish, T., Hagerthey, S., Harvey, J., Leonard, L., McCormick, P., McVoy, C., Noe, G., Nungesser, M., Rutchey, K., Sklar, F., Troxler, T., Volin, J., and Willard, D., 2011, Recent and historic drivers of landscape change in the Everglades ridge, slough, and tree island mosaic: Critical Reviews in Environmental Science and Technology, v. 41, no. 6, p. 344-381. doi: 10.1080/10643389.2010.531219 (on-line abstract of journal article)

McCormick, P.V., Harvey, J.W., Crawford, E.S., 2011, Influence of Changing Water Sources and Mineral Chemistry on the Everglades Ecosystem: Critical Reviews in Environmental Science and Technology, v. 41, no. 6, p. 28-63. doi: 10.1080/10643389.2010.530921 (on-line abstract of journal article)

Skalak, K., Pizzuto, J., Egan, J., and Allmendinger, N., 2011, The geomorphic effects of existing dams and historic dam removals in the U.S. Mid-Atlantic region, in Papanicolaou, T., and Barkdoll, B., eds., Sediment Dynamics Upon Dam Removal: American Society of Civil Engineers Manuals and Reports on Engineering Practice No. 122, p. 83-95.

Wheaton, J.M., Gibbins, C., Wainwright, J., Larsen, L., and McElroy, B., 2011, Preface: Multiscale Feedbacks in Ecogeomorphology: Geomorphology, v. 126, no. 3-4, p. 265-268.

Larsen, L.G., Aiken, G.R., Harvey, J.W., Noe, G.B., and Crimaldi, J.P., 2010, Using fluorescence spectroscopy to trace seasonal DOM dynamics, disturbance effects, and hydrologic transport in the Florida Everglades: Journal of Geophysical Research, v. 115, G03001, doi:10.1029/2009JG001140. (on-line abstract of journal article)

Larsen, L.G. and Harvey, J.W., 2010, How vegetation and sediment transport feedbacks drive landscape change in the Everglades and wetlands worldwide: The American Naturalist, v. 176, no. 3, p. E66-E79. (on-line abstract or on-line article in pdf format, 3923 kb, copyright is not claimed for this article)

Larsen L., Moseman, S., Santoro, A.E., Hopfensperger, K., and Burgin A., 2010, A complex-systems approach to predicting effects of sea level rise and nitrogen loading on nitrogen cycling in coastal wetland ecosystems, in Kemp, P.F., ed. Eco-DAS VIII Symposium Proceedings, ASLO, p. 67-92. doi:10.4319/ecodas.2010.978-0-9845591-1-4.67 (on-line abstract or on-line article in pdf format, 1471 KB, copyright American Society of Limnology and Oceanography with open access provided by the National Science Foundation)

Noe, G.B., Harvey, J.W., Schaffranek, R.W., and Larsen, L.G., 2010, Controls of suspended sediment concentration, nutrient content, and transport in a subtropical wetland: Wetlands, v.30, no. 1, p. 39-54. (on-line abstract of journal article)

O’Connor, B.L., Hondzo, M., and Harvey, J.W., 2010, Predictive modeling of transient storage and nutrient uptake - implications for stream restoration: Journal of Hydraulic Engineering, v. 136, no. 12, p. 1018–1032. doi:10.1061/(ASCE)HY.1943-7900.0000180 (on-line abstract of journal article)

Stonedahl, S.H., Harvey, J.W., Wörman, A., Salehin, M., and Packman, A.I., 2010, A multiscale model for integrating hyporheic exchange from ripples to meanders: Water Resources Research, v. 46, W12539, doi:10.1029/2009WR008865. (on-line abstract of journal article)

Alexander, R.B., Böhlke, J.K., Boyer, E.W., David, M.B., Harvey, J.W., Mulholland, P.J., Seitzinger, S.P., Tobias, C.R., Tonitto, C., Wollheim, W.M., 2009, Dynamic modeling of nitrogen losses in river networks unravels the coupled effects of hydrological and biogeochemical processes: Biogeochemistry, v. 93, p. 91-116. (on-line abstract or on-line paper in pdf format, 850 KB, published at with open access)

Böhlke, J.K., Antweiler, R.C., Harvey, J.W., Laursen, A.E., Smith, L.K., Smith, R.L., and Voytek, M.A., 2009, Multi-scale measurements and modeling of denitrification in streams with varying flow and nitrate concentration in the upper Mississippi River basin, USA: Biogeochemistry, v. 93, p. 117–141. (on-line abstract or on-line paper in pdf format, 959 KB, published at with open access)

Harvey, J.W., and McCormick, P.V., 2009, Groundwater’s Significance to Changing Hydrology, Water Chemistry, and Biological Communities of a Floodplain Ecosystem, Everglades, South Florida: Hydrogeology Journal, v. 17, no. 1, p. 185-201. doi:10.1007/s10040-008-0379-x. (on-line abstract of journal article)

Harvey, J.W., Schaffranek, R.W., Noe, G.B., Larsen, L.G., Nowacki, D.J., and O'Connor, B.L., 2009, Hydroecological factors governing surface water flow on a low-gradient floodplain: Water Resources Research, v. 45, W03421, doi:10.1029/2008WR007129. (on-line abstract or on-line paper in pdf format, 2557 KB, published by the American Geophysical Union, not subject to U.S. copyright)

Hupp, C.R., Pierce, A.R., and Noe, G.B., 2009, Floodplain Geomorphic Processes and Environmental Impacts of Human Alteration Along Coastal Plain Rivers, USA: Wetlands, v. 29, no. 2, p. 413-429. (on-line abstract of journal article)

Larsen, L.G., Harvey, J.W. and Crimaldi, J.P., 2009, Morphologic and Transport Properties of Natural Organic Floc , Water Resources Research, v. 45: W01410, doi:10.1029/2008WR006990. (on-line abstract of journal article)

Larsen, L.G., Harvey, J.W. and Crimaldi, J.P., 2009, Predicting bed shear stress and its role in sediment dynamics and restoration potential of the Everglades and other vegetated flow systems: Ecological Engineering, v. 35, no. 12, p. 1773-1785 . (on-line abstract of journal article)

Larsen, L.G., Harvey, J.W., Noe, G.B. and Crimaldi, J.P., 2009. Predicting Organic Floc Transport Dynamics in Shallow Aquatic Ecosystems: Insights from the Field, the Laboratory, and Numerical Modeling , Water Resources Research, vol. 45: W01411, doi:10.1029/2008WR007221. (on-line abstract of journal article)

Moser, K., Ahn, C., and Noe., G., 2009, The influence of microtopography on soil nutrients in created mitigation wetlands: Restoration Ecology, v. 17, p. 641–651. (on-line abstract of journal article)

Noe, G.B., and Hupp, C.R., 2009, Retention of riverine sediment and nutrient loads by coastal plain floodplains: Ecosystems, v. 12, no. 5, p. 728-746. (on-line abstract or on-line article in pdf format, 404 KB pubished as a U.S. Government work by SpringerLink)

O'Connor, B.L., Hondzo, M., and Harvey, J.W., 2009, Incorporating both physical and kinetic limitations in quantifying dissolved oxygen flux to aquatic sediments: Journal of Environmental Engineering, v. 135, no. 12, p. 1304-1314. (on-line abstract of journal article)

Tobias, C.R., Böhlke, J.K., Harvey, J.W., and Busenberg, E., 2009, A simple technique for continuous measurement of time-variable gas transfer in surface waters: Limnology and Oceanography: Methods, v. 7, p. 185-195. (on-line abstract of journal article)

Cardenas, M.B., Harvey, J.W., Packman, A.I., and Scott, D.T., 2008, Ground-based thermography of fluvial systems at low and high discharge reveals potential complex thermal heterogeneity driven by flow variation and bioroughness: Hydrological Processes, v. 22, p. 980-986. (on-line abstract of journal article)

Huang, Y.H., Saiers, J.E., Harvey, J.W., Noe, G.B., and Mylon., S., 2008. Advection, dispersion, and filtration of fine particles within emergent vegetation of the Florida Everglades: Water Resources Research, v. 44, W04408, doi:10.1029/2007WR006290. (on-line abstract of journal article)

O'Connor B.L., and Harvey, J.W., 2008, Scaling hyporheic exchange and its influence on biogeochemical reactions in aquatic ecosystems: Water Resources Research, v. W12423, doi:10.1029/2008WR007160. (on-line abstact or on-line article in pdf format, 625 KB, published by American Geophysical Union, not subject to U.S. copyright)

Kroes, D.E., Hupp, C.R., and Noe, G.B., 2007, Sediment, nutrient, and vegetation trends along the tidal forested Pocomoke River, Maryland, in Conner, W.H., Doyle, T.W., and Krauss, K.W., eds., Ecology of Tidal Freshwater Swamps of the Southeastern United States: The Netherlands, Springer , p. 113-137.

Larsen, L.G., Harvey, J.W., and Crimaldi, J.P., 2007, A delicate balance: Ecohydrological feedbacks governing landscape morphology in a lotic peatland: Ecological Monographs, v. 77, no. 4, p. 591-614. (on-line abstract of journal article)

McCormick, P.V. and Harvey, J.W., 2007, Influence of changing water sources and mineral chemistry on the Everglades ecosystem: U.S. Geological Survey Administrative Report, U.S. Geological Survey Leetown Science Center, Kearneysville, WV.

Moser, K., Ahn, C., and Noe, G.B., 2007, Characterization of microtopography and its influence on vegetation patterns in created wetlands: Wetlands, v. 27, no 4, p. 1081-1097. (on-line abstract of journal article)

Noe, G.B., and Childers, D.L., 2007, Phosphorus budgets in Everglades wetland ecosystems: The effects of hydrology and nutrient enrichment: Wetlands Ecology and Management, v. 15, p. 189-205. (on-line abstract of journal article)

Noe, G., Fellows, M., and Cornell, J., 2007, Volunteer Monitoring Demonstrates Tree Planting Help Stream Ecosystems: Northern Virginia Soil and Water Conservation District, Conservation Currents, v. 34, no. 2, p. 4-5. (on-line article)

Noe, G.B., Harvey, J.W., and Saiers, J.E., 2007, Characterization of suspended particles in Everglades wetlands: Limnology and Oceanography, v. 52, no. 3., p. 1166-1178. (on-line abstract or on-line article in pdf format, 3584 KB - published by the American Society of Limnology and Oceanography with open access)

Noe, G.B., and C. Hupp, C., 2007, Seasonal variation in nutrient retention during inundation of a short-hydroperiod floodplain: River Research and Applications, v. 23, no. 10 p. 1088-1101. (on-line abstract or on-line journal article in pdf format, 282 KB, published in 2007 by John Wiley & Sons as a U.S. Governement work in the public domain)

Scott, D., Harvey, J., Alexander, R., and Schwarz, G., 2007, Dominance of organic nitrogen from headwater streams to large rivers across the conterminous United States: Global Biogeochemical Cycles, v. 21, GB1003, doi:10.1029/2006GB002730. (on-line abstract or on-line journal article in pdf format, 252 KB - published 2007 by American Geophysical Union, not subject to U.S. copyright)

Tobias, C.R., Böhlke, J.K., and Harvey, J.W., 2007, The oxygen-18 isotope approach for measuring aquatic metabolism in high-productivity waters: Limnology and Oceanography , v. 52, p. 1439-1453. (on-line abstract or on-line journal article in pdf format, 1217 KB - published by the American Society of Limnology and Oceanography with open access)

Wörman, A., Packman, A., Marklund, L., Harvey, J, and S. Stone, 2007, Fractal Topography and Subsurface Water Flows from Fluvial Bedforms to the Continental Shield: Geophysical Research Letters, v. 34, L07402, doi:10.1029/2007GL029426. (on-line abstract of journal article)

Davis, S.E., Childers, D.L., and Noe, G.B., 2006, The contribution of leaching to the rapid release of nutrients and carbon in the early decay of wetland vegetation: Hydrobiologia, v. 569, no. 1, p. 87- 97. (on-line abstract of journal article)

Harvey, J.W., Newlin, J.T., and Krupa, S.L., 2006, Modeling decadal timescale interactions between surface water and ground water in the central Everglades, Florida, USA: Journal of Hydrology, v. 320, p. 400-420. (on-line abstract of journal article)

Hupp, C.R. and Noe, G.B., 2006, Sediment and nutrient accumulation within lowland bottomland ecosystems - An example from the Atchafalaya River Basin, Louisiana: Proceedings Hydrology and Management of Forested Wetlands, American Society of Agricultural and Biological Engineers, p. 175-187.

Smith, L.K., Voytek, M.A., Böhlke, J. K., and Harvey, J.W., 2006, Denitrification in nitrate-rich streams: application of N2:Ar and 15N-tracer methods in intact cores: Ecological Applications, v. 16, p. 2191-2207. (on-line abstract of journal article)

Wörman, A., Packman, A.I., Marklund, L., Harvey, J.W., Stone, S.H., 2006, Exact three-dimensional spectral solution to surface-groudnwater interactions with arbitrary surface topography: Geophysical Research Letters, v. 33, L07402, doi:10.1029/2006GL025747 (on-line abstract of journal article)

Gaiser, E. E., Trexler, J., Richards, J., Childers, D., Lee, D., Edwards, A.L., Scinto, L., Jayachandran, K., Noe, G., and Jones, R., 2005, Cascading ecological effects of low-level phosphorus enrichment in the Florida Everglades: Journal of Environmental Quality, v. 34, p. 717-723. (on-line abstract of journal article)

Gooseff, M.N., Bencala, K.E., Scott, D.T., Runkel, R.L., and McKnight, D.M., 2005, Sensitivity analysis of conservative and reactive stream transient storage models applied to field data from multiple-reach experiments: Advances in Water Resources, v. 28, p. 479-492. (on-line abstract of journal article)

Harvey, J.W., Newlin, J.T., Krest, J.M., Choi, J., Nemeth, E.A., and Krupa, S.L., 2005, Surface-water and ground-water interactions in the central Everlgades, Florida: U.S. Geological Survey Scientific Investigations Report 2004-5069, 88 p.

Harvey, J.W., Saiers, J.E., and Newlin, J.T., 2005, Solute transport and storage mechanisms in wetlands of the Everglades, South Florida, Water Resources Research, v. 41, no. 5, W05009, doi:10.1029/2004WR003507. (on-line abstract of journal article)

Noe, G.B., and Hupp, C.R., 2005, Carbon, nitrogen, and phosphorus accumulation in floodplains of Atlantic Coastal Plain rivers, USA: Ecological Applications, v. 15, p.1178-1190. (on-line abstract of journal article)

Böhlke, J.K, Harvey, J.W., and Voytek, M.A., 2004, Reach-scale isotope tracer experiment to quantify denitrification and related processes in a nitrate-rich stream, midcontinent United States: Limnology and Oceanography, v. 49, no. 3, p. 821-838. (on-line abstract of journal article or on-line paper in pdf format)

Harvey, J.W., Krupa, S.L., and Krest, J.M., 2004, Ground water recharge and discharge in the central Everglades: Ground Water, v. 42, no. 7, p. 1090-1102. (on-line abstract)

Lee, J.K., Roig, L.C., Jenter, H.L., and Visser, H.M., 2004, Drag coefficients for modeling flow through emergent vegetation in the Florida Everglades: Ecological Engineering, v. 22, p. 237-248. (on-line summary plus)

American Society of Limnology and Oceanography, 2003, Emerging Research Questions for Limnology - Study of Inland Waters: Workshop, Dec, 2002, American Society of Limnology and Oceanography, Waco, Texas, 48 p.

Gray, J.R., Patiño, Eduardo, Rasmussen, P.P., Larsen. M.C., Melis, T.S., Topping, D.J., and Alamo, C.F., 2003, Evaluation of sediment surrogate technologies for computation of suspended-sediment transport: Proceedings of the 1st International Yellow River Forum on River Basin Management, Zhengzhou, Henan Province, China, the Yellow River Conservancy Publishing House, v. III, p. 314-323.

Grimm, N.B., Gergel, S.E., McDowell, W.H., Boyer, E.W., Dent, C.L., Groffman, P.M., Hart, S.C., Harvey, J.W., Johnston, C.A., Mayorga, E., McClain, M.E., and Pinay, G., 2003, Merging aqatic and terrestrial perspectives of nutrient biogeochemistry: Oecologia, v. 137, no. 4, p. 485-501. (on-line abstract)

Harvey, J.W., Conklin, M.H., and Koelsch, R.S., 2003, Predicting changes in hydrologic retention in an evolving semi-arid stream: Advances in Water Resources, v. 26, p. 939-950. (on-line abstract)

Krest, J.M. and Harvey, J.W., 2003, Using natural distributions of short-lived radium isotopes to quantify groundwater discharge and recharge: Limnology and Oceanography v. 48 no. 1, p. 290-298. (on-line abstract or article in pdf format)

Melis, T.S., Topping, D.J., and Rubin, D.M., 2003, Testing laser-based sensors for continuous in situ monitoring of suspended sediment in the Colorado River, Arizona, in Bogen, J., Fergus T., and Walling, D.E., eds., Erosion and Sediment Transport Measurement in Rivers: Technological and Methodological Advances (Proceedings of the Oslo Workshop, June 2002): IAHS Publication 283, p. 21-27. (on-line abstract)

McClain, M.E., Boyer, E.W., Dent, C.L. Gergel, S.E., Grimm, N.B., Groffman, P.M., Hart, S.C., Harvey, J.W., Johnston, C.A., Mayorga, E., McDowell, W.H., and Pinay, G., 2003, Biogeochemical hot spots and hot moments at the interface of terrestrial and aquatic ecosystems: Ecosystems, v. 6, no. 4, p. 301-312. (on-line abstract)

Noe, G.B., Scinto, L.J., Taylor, J., Childers, D.L., and Jones, R.D., 2003, Phosphorus cycling and partitioning in oligotrophic Everglades wetland ecosystems: A radioisotope study: Freshwater Biology, v. 48, no. 11, p. 1993-2008. (on-line abstract)

Scott, D.T., Gooseff, M.N., Bencala, K.E., and Runkel,R.L., 2003, Automated calibration of a stream solute transport model: implications for interpretation of biogeochemical parameters:Journal of the North American Benthological Society, v. 22, no. 4, p. 492-510. (on-line abstract)

Topping, D.J., Schmidt, J.C., and Vierra, L.E., Jr., 2003, Computation and analysis of the instantaneous-discharge record for the Colorado River at Lees Ferry, Arizona.May 8, 1921, through September 30, 2000: U.S. Geological Survey Professional Paper 1677. (on-line abstract or on-line paper in pdf format, 54.6MB)

Judson W Harvey (professional profile)
U.S. Geological Survey, 430 National Center, 12201 Sunrise Valley Drive, Reston, VA 20192
Telephone: 703-648-5876

Larsen, Laurel (professional profile)
U.S. Geological Survey, 430 National Center, 12201 Sunrise Valley Drive, Reston, VA 20192
Telephone: 703-648-5891

Harry L Jenter (professional profile)
U.S. Geological Survey, 430 National Center, 12201 Sunrise Valley Drive, Reston, VA 20192
Telephone: 703-648-5916

For information on additional projects in the National Research Program, see Indexes to NRP projects and bibliographies.

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