University of Wisconsin–Madison


Crawford, J. T., L.C. Loken, W.E. West, B. Crary, S.A. Spawn, N. Gubbins, S.E. Jones, R.G. Striegl, and E.H. Stanley. 2017. Spatial heterogeneity of within-stream methane concentrations. Journal of Geophysical Research Biogeosciences, accepted.

Collins, S.M., S.K. Oliver, J.F. Lapierre, E.H. Stanley, J. R. Jones, T. Wagner, and P.A. Soranno. 2017. Lake nutrient stoichiometry is less predictable than nutrient concentrations at regional and sub-continental scales. Ecological Applications, accepted.

Crawford, J.T., E.H. Stanley, M.M. Dornblaser, and R.G. Striegl. 2016. CO2 time series patterns in contrasting headwater streams of the Northern Hemisphere. Aquatic Sciences 10.1007/s00027-016-0511-2.

Jones, J.B. and E.H. Stanley, editors. 2016. Streams in a Changing Environment. Academic Press/Elsevier, London.

Jones, J.B. and E.H. Stanley 2016. Synthesis and conclusions. Pages 525-533 in J.B. Jones and E.H. Stanley, editors. Streams in a Changing Environment. Academic Press/Elsevier, London.

Stanley, E.H., R.A. Sponseller, and J.B. Heffernan. 2016. Landscape and regional stream ecology. Pages 389-415 in J.B. Jones and E.H. Stanley, editors. Streams in a Changing Environment. Academic Press/Elsevier, London.

Hampton, S.E., A.W.E. Galloway, S.M. Powers, T. Ozersky, K.H. Woo, R.D. Batt, S.G. Labou, C.M. O’Reilly, S. Sharma, N.R. Lottig, E.H. Stanley, R.L. North, J.D. Stockwell, R. Adrian, G.A. Weyhenmeyer, L. Arvola, H.M. Baulch, I. Bertani, L.L. Bowman, Jr., C.C. Carey, J. Catalan, W. Colom-Montero, L.M. Domine, M. Felip, I. Granadoso, C. Gries, H.P. Grossart, J. Haberan, M. Haldna, B. Hayden, S.N. Higgins, J.C. Jolley, K.K. Kahilainen, E. Kaup, M.J. Kehoe, S. MacIntyre, A.W. Mackay, H.L. Mariash, R.M. McKay, B. Nixdorf, P. Nõges, T. Nõges, M. Palmer, D.C. Pierson, D.M. Post, M.J. Pruett, M. Rautio, J. S. Read, S.L. Roberts, J. Rücker, S. Sadro, E.A. Silow, D.E. Smith, R.W. Sterner, G.E.A. Swann, M.A. Timofeyev, M. Toro, M.R. Twiss, R.J. Vogt, S.B. Watson, E.J. Whiteford, and M.A. Xenopoulos. 2016. Ecology under lake ice. Ecology Letters: accepted.

Gries, C., M.R. Gahler, P.C. Hanson, T.K. Kratz, and E.H. Stanley. 2016. Information management at the North Temperate Lakes Long-Term Ecological Research site – successful support of research in a large, diverse, and long running project. Ecological Informatics 10.1016/j.ecoinf.2016.08.007

Oliver, S.K., P.A. Soranno, C.E. Fergus, T. Wagner, L.A. Winslow, C.E. Scott, K.E. Webster, J.A. Downing, and E.H. Stanley. 2016. Prediction of lake depth across a 17-state region in the U.S. Inland Waters 6:314-324.

Crawford, J.T. and E.H. Stanley. 2016. Controls on methane concentrations and fluxes in streams draining human-dominated landscapes. Ecological Applications 26:1581-1591.

Stanley, E.H., N.J. Casson, S.T. Christel, J.T. Crawford, L.C. Loken, and S.K. Oliver. 2016. The ecology of methane in streams and rivers: patterns, controls, and global significance. Ecological Monographs 86: 146-171.

Crawford, J.T., L.C. Loken, E.H. Stanley, E.G. Stets, M.M. Dornblaser, and R.G. Striegl. 2016. Eutrophication and sediments control greenhouse gas emissions from the Upper Mississippi River. Geophysical Research Letters DOI: 10.1002/2015GL067599

Loken, L.C., G.E. Small, J.C. Finlay, R.W. Sterner, and E.H. Stanley. 2016. Nitrogen cycling in a freshwater estuary. Biogeochemistry127:199-216.

Soranno, P.A., E.G. Bissell, K.S. Cheruvelil, S.T. Christel, S.M. Collins, C.E. Fergus, C.T. Filstrup, J.-F. Lapierre, N.R. Lottig, S.K. Oliver, C.E. Scott, N.J. Smith, S. Stopyak, S. Yuan, M.T Bremigan, J.A. Downing, C. Gries, E.N. Henry, N.K. Skaff, E.H. Stanley, C.A. Stow, P.-N. Tan, T. Wagner, and K.E. Webster. 2015. Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science through data reuse. GigaScience 4: 10.1186/s13742-015-0067-4.

Crawford, J.T., M.M. Dornblaser, E.H. Stanley, D.W. Clow, and R.G. Striegl. 2015. Source limitation of carbon gas emissions in high-elevation mountain streams and lakes. Journal of Geophysical Research- Biogeosciences 120:10.1002/2014JG002861.

Crawford, J.T., L.C. Loken, N.J. Casson, C.Smith, A.G. Stone, and L.A. Winslow. 2015. High-speed limnology: Using advanced sensors to investigate spatial varibility in biogeochemistry and hydrology. Environmental Science and Technology,49:442-450.

Hampton, S.E., M.V. Moore, T. Ozersky, E.H. Stanley, C.M. Poleshenski, and A.W.E. Galloway. 2015. Heating up a cold subject: prospects for under‐ice research in lakes. Journal of Plankton Research 37:277-284.

Hanson, P.C., M.L. Pace, S.R. Carpenter, J.J. Cole, and E.H. Stanley. 2015. Integrating landscape carbon cycling: research needs for resolving organic carbon budgets. Ecosystems 18: 363–375.

Winslow, L.A., J.S. Read, P.C. Hanson, and E.H. Stanley. 2015. Does lake size matter?  Combining morphology and process modeling to examine the contribution of lake classes to population-scale processes. Inland Waters 5:7-14.

Filstrup, C.T., T. Wagner, P.A. Soranno, E. H. Stanley, C.A. Stow, K.E. Webster, and J.A. Downing. 2014. Regional variability among nonlinear chlorophyll-phosphorus relationships in lakes. Limnology and Oceanography 59:1691-1703.

Powers, S.M., D.M. Robertson, and E.H. Stanley. 2014. Effects of lakes and reservoirs on annual nutrient and sediment export in agricultural and forested landscapes. Hydrological Processes 28:5919-5937.

Crawford, J.T., E.H. Stanley, S.A. Spawn, J.C. Finlay, L.C. Loken, and R.G. Striegl. 2014. Ebullitive methane emissions from oxygenated wetland streams. Global Change Biology 20:3408-3422.

Crawford, J.T., N.R. Lottig, E.H. Stanley, J.F. Walker, P.C. Hanson, J.C. Finlay, and R.G. Striegl. 2014. CO2 and CH4 emissions from streams in a lake-rich landscape: Patterns, controls and regional significance. Global Biogeochemical Cycles 28:197-210.

Crawford, J.T. and E.H. Stanley. 2014. Distinct fluvial patterns of a headwater stream network underlain by discontinuous permafrost. Arctic, Antarctic, and Alpine Research 46:52-62.

Orr, C.H., K.I. Predick, K.L. Rogers, and E.H. Stanley. 2014. Spatial autocorrelation of denitrification in a restored and a natural floodplain. Wetlands 34:89-100.

Soranno, P.A., K.S. Cheruvilil, E.G. Bissell, M.T. Bremigan, J.A. Downing, C.E. Fergus, C.T. Filstrup, N.R. Lottig, E.N. Henry, E.H. Stanley, C.A. Stow, P.-N. Tang, T. Wagner, and K.E. Webster. 2014. Cross-scale interactions: quantifying multi-scaled cause-effect relationships in macrosystems. Frontiers in Ecology and the Environment 12:65-73.

Watras, C.J., J.S. Read, K.D. Holman, Z. Liu, Y.-Y. Song, A.J. Watras, S. Morgan, and E. H. Stanley. 2014. Decadal oscillation of lakes and aquifers in the upper Great Lakes region of North America: hydroclimatic implications. Geophysical Research Letters 41:456-462.

Hanson, P.C., I. Buffam, J. Rusak, E.H. Stanley, and C. Watras. 2014. Quantifying lake allochthonous organic carbon budgets using a simple equilibrium model. Limnology and Oceanography 59:167-181.

Winslow, L.A., J.S. Read, P.C. Hanson, and E.H. Stanley. 2014. Lake shoreline in the contiguous United States: quantity, distribution and sensitivity to observation resolution. Freshwater Biology 59:213-223.

Lottig, N.R., I. Buffam, and E.H. Stanley. 2013. Comparisons of wetland and drainage lake influences on stream dissolved carbon concentrations and yields in a north temperate lake-rich region. Aquatic Sciences 75:619-630.

Crawford, J.T., R.G. Striegl, K.P. Wickland, M.M. Dornblaser, and E.H. Stanley. 2013. Emissions of carbon dioxide and methane from a headwater stream network of interior Alaska. Journal of Geophysical Research Biogeosciences 118:482-494.

Powers, S.M., J.P. Julian, M.W. Doyle, and E.H. Stanley. 2013. Retention and transport of nutrients in a mature agricultural impoundment. Journal of Geophysical Research Biogeosciences 118:91-103.

Stanley, E.H. 2013. Understanding the ecological effects of dams. Pages 253-258 in K.C. Weathers, D.L. Strayer, and G.E. Likens, editors. Fundamentals of Ecosystem Science. Academic Press.

Shade, A., J.S. Read, N.D. Youngblut, N. Fierer, R. Knight, T.K. Kratz, N.R. Lottig, E.E. Roden, E.H. Stanley, J. Stombaugh, R.J. Whitaker, C.H. Wu, and K.D. McMahon. 2012. Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME Journal 6:2153–2167.

Lottig, N.R., E.H. Stanley, and J.T. Maxted. 2012. Assessing the influence of upstream drainage lakes on fluvial organic carbon in a wetland rich region. Journal of Geophysical Research Biogeosciences 117:G03011, doi:10.1029/2012JG001983.

Powers, S.M., R.A. Johnson, and E.H. Stanley. 2012. Nutrient retention and the problem of hydrologic disconnection in streams and wetlands. Ecosystems 15:435-449.

Robertson, G.P., N. Brokaw, S.L. Collins, H.W. Ducklow, D.R. Foster, T.L. Gragson, C. Gries, S.K. Hamilton, A.D. McGuire, J.C. Moore, E.H. Stanley, R.B. Waide and M.W. Williams. 2012. Long term ecological research in a human dominated world. BioScience 62:342-353.

Stanley, E.H., S.M. Powers, N.R. Lottig, I. Buffam, and J.T. Crawford. 2012. Contemporary changes in dissolved organic carbon of human-dominated rivers: Is there a role for DOC management? Freshwater Biology 57 (Suppl. 1): 26–42.

Carpenter, S.R., E.H. Stanley, and M.J. Vander Zanden. 2011. State of the world’s freshwater ecosystems: physical, chemical, and biological changes. Annual Review of the Environment and Resources 36:75-99.

Baulch, H.M., E.H. Stanley, and E.S. Bernhardt. 2011. Can algal uptake stop NO3 pollution? Nature 477: doi:10.1038/nature10418.

Lottig, N.R., E.H. Stanley, P.C. Hanson, and T.K. Kratz. 2011. Comparison of regional stream and lake chemistry: Differences, similarities, and potential drivers. Limnology and Oceanography 56:1551-1562.

Hanson, P.C., D.P. Hamilton, E.H. Stanley, N. Preston, O. Langman, and E.L. Kara. 2011. Fate of allochthonous dissolved organic carbon in lakes: A quantitative approach.  PLoS ONE 6: e21884. doi:10.1371/journal.pone.0021884.

Julian, J.P, S.Z. Seegert, S.M. Powers, E.H. Stanley, and M.W. Doyle. 2011. Light as a first-order control on ecosystem structure in a small Midwestern stream. Ecohydrology 4:422-432.

Buffam, I., M.G. Turner, A. Desai, P.C. Hanson, J.A. Rusak, N.R. Lottig, E.H. Stanley, and S.R. Carpenter. 2011. Integrating aquatic and terrestrial components to construct a complete carbon budget for a north temperate lake district. Global Change Biology 17:1193–1211.

Stanley, E.H. and A.K. Ward. 2010. Effects of vascular plants on seasonal pore water carbon dynamics in a lotic wetland. Wetlands 30:889-900.

Predick, K.I. and E.H. Stanley. 2010. Influence of vegetation and seasonal flow patterns on hyporheic nitrogen retention in a 7th-order river. Journal of the North American Benthological Society 29:904-917.

Stanley, E.H., S.M. Powers, and N.R. Lottig. 2010. The evolving legacy of disturbance in stream ecology: concepts, contributions and coming challenges. Journal of the North American Benthological Society 29:67-83.

Powers, S.M., E.H. Stanley, and N.R. Lottig. 2009. Quantifying phosphorus uptake using pulse and steady-state approaches in streams. Limnology and Oceanography Methods 7:498-508.

Solomon, C.T., E.R. Hotchkiss, J.M. Moslemi, A.J. Ulseth, E.H. Stanley, R.O. Hall, and A.S. Flecker. 2009. Sediment size and nutrients regulate denitrification in a tropical stream. Journal of the North American Benthological Society 28:480–490.

Stanley, E.H. 2009. Lake levels and drought indices in northern Wisconsin: data, graphs, and photographs.  Ecological Society of American EcoEd Digital Library, Ecological Society of America. http://

Julian, J.P., E.H. Stanley, and M.W. Doyle. 2008. Basin-scale consequences of agricultural land use on benthic light availability and primary production along a 6th-order temperate river. Ecosystems 11:1091-1105.

Julian, J.P., M.W. Doyle, S.M. Powers, E.H. Stanley and J.A. Riggsbee. 2008. Optical water quality in rivers. Water Resources Research 44: W10411, doi:10.1029/2007WR006457.

Julian, J.P., M.W. Doyle, and E.H. Stanley. 2008. Empirical modeling of light availability in rivers. Journal of Geophysical Research- Biogeosciences 11:G03022, doi 10.1029/2007JG000601.

Stanley, E.H. and J.T. Maxted. 2008. Changes in the dissolved nitrogen pool across land cover gradients in Wisconsin streams. Ecological Applications 18:1579-1590.

Doyle, M.W., E.H. Stanley, D. Havlick, M.J. Kaiser, G. Steinbach, W. Graf, and G. Galloway. 2008. Aging infrastructure and ecosystem restoration. Science 319:286-287.

Orr, C.H., S.J. Kroiss, K.L. Rogers, and E.H. Stanley. 2008. Downstream benthic responses to small dam removal in a coldwater stream. River Research and Applications 24:804-822.

Turner, M. G., E. H. Stanley, M. Bürgi and D. J. Mladenoff.  2008. Changes in the Wisconsin River and its floodplain.  Pages 229-249 in D. M. Waller and T. P. Rooney, editors. The vanishing present: ecological change in Wisconsin.  University of Chicago Press.

Orr, C.H., E.H. Stanley, K.A. Wilson and J.C. Finlay. 2007. Effects of restoration and reflooding on soil denitrification in a leveed Midwestern floodplain.  Ecological Applications 17:2365-2376.

Stanley, E.H., M.J. Catalano, N. Mercado-Silva, and C.H. Orr. 2007. Effects of dam removal on brook trout in a Wisconsin stream. River Research and Applications 23:792-798.

Watters, J.R. and E.H. Stanley. 2007 Stream channels in peatlands: the role of biological processes in controlling channel form. Geomorphology 89:97-110.

Lottig, N.R. and E.H. Stanley. 2007. Benthic sediment influence on dissolved phosphorus concentrations in a headwater stream. Biogeochemistry 84:297-309.

Carpenter, S.R., B.J. Benson, R. Biggs, J.W. Chipman, J.A. Foley, S.A. Golding, R.B. Hammer, P.C. Hanson, P.T.J. Johnson, A.M. Kamarainen, T.K. Kratz, R.C. Lathrop, K.D. McMahon, B. Provencher, J.A. Rusak, C.T. Solomon, E.H. Stanley, M.G. Turner, M.J. Vander Zanden, C.-H. Wu and H. Yuan. 2007. Understanding regional change: Comparison of two lake districts. BioScience 57:323-335.

Doyle, M.W. and E.H. Stanley. 2006. Exploring potential spatial-temporal links between fluvial geomorphology and nutrient-periphyton dynamics in streams using simulation models. Annals of the Association of American Geographers 96:687-698.

Kondolf, G. M., A. J. Boulton, S. O’Daniel, G. C. Poole, F. J. Rahel, E. H. Stanley, E. Wohl, A. Bang, J. Carlstrom, C. Cristoni, H. Huber, S. Koljonen, P. Louhi and K. Nakamura 2006. Process-based ecological river restoration: visualizing three-dimensional connectivity and dynamic vectors to recover lost linkages. Ecology and Society 11:5. [online] URL:

Orr, C.H., K.L. Rogers, and E.H. Stanley. 2006. Channel geomorphology and P uptake following removal of a small dam. Journal of the North American Benthological Society 25:556-568.

Hanson, P.C., S.R. Carpenter, D.E. Armstrong, E.H. Stanley, and T.K. Kratz. 2006. Drivers of lake dissolved inorganic carbon and dissolved oxygen across scales from days to decades. Ecological Monographs 76:343-363.

Orr, C.H. and E.H. Stanley. 2006. Vegetation development and restoration potential of drained reservoirs following dam removal in Wisconsin. River Research and Applications 22:281-295.

Forshay, K.J. and E.H. Stanley. 2005. Rapid nitrate loss and denitrification in a temperate river floodplain. Biogeochemistry 75:43-64.

Doyle, M.W., E.H. Stanley, D.L. Strayer, R.B. Jacobson, and J.C. Schmidt. 2005. Dominant discharge analysis of ecological processes in streams. Water Resources Research 41:W11411, doi 10.1029/2005WR00422.

Doyle, M.W., E.H. Stanley, C.H. Orr, A.R. Selle, S.A. Sethi, and J.M. Harbor. 2005. Stream ecosystem response to small dam removal: lessons from the Heartland. Geomorphology 71: 227-244.

Gergel, S.E., S.R. Carpenter, and E.H. Stanley. 2005. Do dams and levees impact nitrogen cycling? Simulating the effects of flood alterations on floodplain denitrification. Global Change Biology 11:1352-1367.

Jansson, R., H. Backx, A.J. Boulton, M. Dixon, D. Dudgeon, F. Hughes, K. Nakamura, E. Stanley, and K. Tockner 2005. Stating mechanisms and refining criteria for ecologically successful river restoration:  A comment on Palmer et al. (2004).  Journal of Applied Ecology 42:218-222.

Kang, H. and E.H. Stanley. 2005. Effects of levees on soil microbial activities in a large river floodplain. River Research and Applications 21:19-25.

Doyle, M. and Stanley, E. 2005. Stream ecosystem response to experimental dam removals. Pages 1-12 in G.E. Moglen (ed.), Managing Watersheds for Human and Natural Impacts: pp. 1-12. doi: 10.1061/40763(178)20

Sethi, S.A., A.R. Selle, M.W. Doyle, E.H. Stanley, and H.E. Kitchel. 2004. Response of unionid mussels to dam removal in Koshkonong Creek, Wisconsin (U.S.A.). Hydrobiologia 525:157-165.

Miller, J. R., M. G. Turner, E. A. H. Smithwick, C. L. Dent, and E. H. Stanley.  2004. Spatial extrapolation: the science of predicting ecological patterns and processes. BioScience 54:310-320.

Stanley, E.H., S.G. Fisher, and J.B. Jones. 2004. Effects of water loss on primary producers: a landscape-scale model. Aquatic Sciences 66:130-138.

Nilsson, C., J.E. Pizzuto, G.E. Moglen, M.A. Palmer, E.H. Stanley, N.E. Bockstael, and L.C. Thompson. 2003. Ecological forecasting and urbanized streams: challenges for economists, hydrologists, geomorphologists, and ecologists.  Ecosystems 6:659-674.

Kang, H., E.H. Stanley, and S.S. Park. 2003. A sensitive method for the measurement of ammonium in soil extract and water using an OPA compound. Communications in Soil Science and Plant Analysis 34:2193-2201.

Doyle, M.W., A.R. Selle, J.M. Stofleth, E.H. Stanley, and J.M. Harbor. 2003.  Predicting the depth of erosion following dam removal using a bank stability model. International Journal of Sediment Research 18:128-134.

Doyle, M.W., E.H. Stanley, and J.M. Harbor. 2003. Hydrogeomorphic controls on phosphorus retention in streams. Water Resources Research 39:1147, doi 10.1029/2003WR002038.

Jones, J.B., E.H. Stanley, and P.J. Mulholland. 2003. Increased alkalinity in the Mississippi River. Science 302:985-986.

Jones, J.B., E.H. Stanley and P.J. Mulholland. 2003. Long-term decline in carbon dioxide supersaturation in rivers across the contiguous United States. Geophysical Research Letters 30: 10.1029/2003GL017056

Freeman, R.E., E.H. Stanley, and M.G. Turner. 2003. Analysis and conservation implications of landscape change in the floodplain of the Wisconsin River, USA. Ecological Applications 13:416-431.

Doyle, M.W., J.M. Harbor, and E.H. Stanley. 2003. Towards policies and decision-making for dam removal. Environmental Management 31:453-465.

Stanley, E.H. and M.W. Doyle. 2003. Trading off: the ecological effects of dam removal. Frontiers in Ecology and the Environment 1:15-22.

Doyle, M.W., E.H. Stanley, and J.M. Harbor. 2003. Channel adjustments following two dam removals in Wisconsin. Water Resource Research 39:1011, doi 10.1029/2002WR001714.

Benda, L.E., N. L. Poff, C. Tague, M.A. Palmer, J. Pizzuto, N. Bockstael, S. Cooper, E. Stanley, and G. Moglen. 2002.  Avoiding train wrecks in the use of science in environmental problem solving. BioScience 52:1127-1136.

Stanley, E.H. and M.W. Doyle. 2002. A geomorphic perspective on nutrient retention following dam removal. BioScience 52:693-701.

Doyle, M.W., E.H. Stanley, and J.M. Harbor. 2002. Assessing probable channel response to dam removal using geomorphic analogies.  Journal of the American Water Resources Association 38:1567-1580.

Gergel, S.E., M.G. Turner, J.R. Miller, J.M. Melack, and E.H. Stanley. 2002. Landscape indicators of human impacts to river-floodplain systems. Aquatic Sciences 64:118-128.

Stanley, E.H., M.A. Luebke, M.W. Doyle, and D.W. Marshall. 2002. Short-term changes in channel form and macroinvertebrate communities following low-head dam removal. Journal of the North American Benthological Society 21:172-187.

Doyle, M.W., E.H. Stanley, M.A. Luebke, and J.M. Harbor. 2000. Dam removal: physical, biological, and societal considerations. American Society of Civil Engineering Joint Conference on Water Resources Engineering and Water Resources Planning and Management, Minneapolis, MN.

Stanley, E.H. and A.J. Boulton. 2000. River size as a factor in conservation. Pages 403-413 in P.J. Boon, B.R. Davies, and G.E. Petts (eds.), Global perspectives on river conservation: science, policy, and practice. John Wiley and Sons.

Boulton, A.J. F. Sheldon, M.C. Thoms, and E.H. Stanley. 2000. Problems and constraints in managing rivers with contrasting flow regimes.  Pages 415-430 in P.J. Boon, B.R. Davies, and G.E. Petts (eds.), Global perspectives on river conservation: science, policy, and practice. John Wiley and Sons.

Stanley, E.H. and J.B. Jones, Jr. 2000. Surface-subsurface interactions: past, present, and future. Pp. 405-417 in J.B. Jones, Jr. and P.J. Mulholland (eds.), Streams and Groundwater. Academic Press.

Boulton, A.J., S. Findlay, P. Marmonier, E.H. Stanley, and H.M. Valett. 1998. The functional significance of the hyporheic zone in streams and rivers.  Annual Review of Ecology and Systematics 29:59-81.

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