Journal Articles Applying National Aquatic Resource Survey Data

In addition to development of the National Aquatic Resource Surveys (NARS) reports on the condition of the nation's waters, the data from the surveys are used by scientists and researchers to conduct additional research.

The following is a collection of citations of peer-reviewed scientific journal articles that apply NARS data. These articles are organized by water resource type.

On this page:

Coastal Waters and the Great Lakes
Lakes
Rivers and Streams
Wetlands

The following links exit the site

Coastal Waters and the Great Lakes

Lakes

2025

Handler, A. M., Weber, M., Dumelle, M., Jansen, L. S., Carleton, J. N., Schaeffer, B. A., Paulsen, S. G., Barnum, T., Rea, A. W., Neale, A., & Compton, J. E. (2025). Ecological condition of mountain lakes in the conterminous United States and vulnerability to human development. Ecological Indicators, 173, 113402. https://doi.org/10.1016/j.ecolind.2025.113402

Mitchell, R.M, A.T. Herlihy, R.M. Hughes. 2025 Striving for consistency in a national lake assessment: Defining reference status and littoral macroinvertebrate condition in lakes across the conterminous United States. Ecological Indicators. 170. 112992. https://doi.org/10.1016/j.ecolind.2024.112992

2024

Bevier, C. R., Cole, F. R., Gimond, M., & Rueger, B. F. (2024). The Influence of Shoreline Residential Development on Riparian and Littoral Habitats in the Belgrade Lakes of Maine. bioRxiv, 2024-08.

Brehob, M. M., Pennino, M. J., Handler, A. M., Compton, J. E., Lee, S. S., & Sabo, R. D. (2024). Estimates of lake nitrogen, phosphorus, and chlorophyll‐a concentrations to characterize harmful algal bloom risk across the United States. Earth's Future, 12(8), e2024EF004493.

Dietrich, M., Golden, Heather, Christensen, Jay, Lane, Charles, and Dumelle, M. 2024. Lake chlorophyll-a linked to upstream nutrients across the Conterminous United States. Environmental Science & Technology Letters, 11(12), https://pubs.acs.org/doi/10.1021/acs.estlett.4c00938

Le Noac’h, P., & Beisner, B. E. (2024). A database of nutritional strategies of nanoplankton genera present in North American lake surface waters. Journal of Plankton Research, fbae035.

Meyer, M. F., Topp, S. N., King, T. V., Ladwig, R., Pilla, R. M., Dugan, H. A., ... & Zwart, J. A. (2024). National-scale remotely sensed lake trophic state from 1984 through 2020. Scientific data, 11(1), 77.

Nord, M. A., Maier, M. A., Bijak, A. L., Crane, J. L., & Pollard, A. I. (2024). Assessment of recent lake sediment conditions in the conterminous U.S. Science of The Total Environment, 956, 177315. https://doi.org/10.1016/j.scitotenv.2024.177315

2023

Bonilla, Sylvia, et al. "Nutrients and not temperature are the key drivers for cyanobacterial biomass in the Americas." Harmful Algae 121 (2023): 102367.

Deeds, J., Amirbahman, A., Hugger, K., Kaufmann, P.R., Matthews, L.J., Merrell, K., Norton, S.A. (2023) Assessment indices of littoral habitat condition for lakes in Maine and New England, United States, Lake and Reservoir Management. https://doi.org/10.1080/10402381.2023.2207490

Dumelle, M., Kincaid, T., Olsen, A. R., & Weber, M. 2023. spsurvey: Spatial Sampling Design and Analysis in R. Journal of Statistical Software, 105(1), 1–29.

Dumelle, M., Ver Hoef, J. M., Handler, A., Hill, R. A., Higham, M., & Olsen, A. R. (2023). Modeling lake conductivity in the contiguous United States using spatial indexing for big spatial data. Spatial Statistics, 100808.

Handler, A. M., Compton, J.E. Hill, R. A., Leibowitz, S. G., & Schaeffer, B. A. (2023). Identifying lakes at risk of toxic cyanobacterial blooms using satellite imagery and field surveys across the United States. Science of the Total Environment, 161784.

Hill, R. A., Moore, C. C., Doyle, J. M., Leibowitz, S. G., Ringold, P. L., & Rashleigh, B. (2023). Estimating biotic integrity to capture existence value of freshwater ecosystems. Proceedings of the National Academy of Sciences, 120(18), e2120259119.

Mamun, S., Castillo-Castillo, A., Swedberg, K., Zhang, J., Boyle, K.J., Cardoso, D., Kling, C.L., Nolte, C., Papenfus, M., Phaneuf, D. and Polasky, S., 2023. Valuing water quality in the United States using a national dataset on property values. Proceedings of the National Academy of Sciences, 120(15), p.e2210417120.

Merder, J., Harris, T., Zhao, G., Stasinopoulos, D. M., Rigby, R. A., & Michalak, A. M. (2023). Geographic redistribution of microcystin hotspots in response to climate warming. Nature Water, 1-11.

Pilla, R. M., & Griffiths, N. A. (2023). Integrating Reservoirs into the Dissolved Organic Matter Versus Primary Production Paradigm: How Does Chlorophyll-a Change Across Dissolved Organic Carbon Concentrations in Reservoirs?. Ecosystems, 1-14.

Sabo, R. D., Pickard, B., Lin, J., Washington, B., Clark, C. M., Compton, J. E., ... & Stoddard, J. L. 2023. Comparing drivers of spatial variability in US lake and stream phosphorus concentrations. Journal of Geophysical Research: Biogeosciences, e2022JG007227.

2022

Dumelle, M., Higham M., Ver Hoef J. M., Olsen, A. R., Madsen, L. 2022. "A comparison of design‐based and model‐based approaches for finite population spatial sampling and inference." Methods in Ecology and Evolution 13.9: 2018-2029.

Fergus, C.E., Brooks, J.R., Kaufmann, P.R., Pollard, A.I., Mitchell, R., Geldhof, G.J., Hill, R.A., Paulsen, S.G., Ringold, P., Weber, M. 2022. Natural and anthropogenic controls on lake water-level decline and evaporation-to-inflow ratio in the conterminous United States. Limnol. Oceanogr. 67, 1484–1501.

2021

Crane, J.L. 2021. Distribution and toxic potential of alkylphenols, nonylphenol ethoxylates, and pyrethroids in Minnesota, USA lake sediments. Science of the Total Environment 776:145974.

Crane, J.L., Bijak, A.L., Maier, M.A. and Nord, M.A., 2021. Development of current ambient background threshold values for sediment quality parameters in US lakes on a regional and statewide basis. Science of The Total Environment, 793, p.148630.

Fergus, C.E., J.R. Brooks, P.R. Kaufmann, A.I. Pollard, A.T. Herlihy, S.G. Paulsen, and M.H. Weber. 2021. National framework for ranking lakes by potential for anthropogenic hydro-alteration. Ecological Indicators 122:107241.

Frei, R.J., G.M. Lawson, A.J. Norris, G. Cano, M.C. Vargas, E. Kujanpää, A. Hopkins, B. Brown, R. Sabo, J. Brahney, and B.W. Abbott. 2021. Limited progress in nutrient pollution in the U.S. caused by spatially persistent nutrient sources. PLoS ONE 16(11):e0258952.

Manning, D.W.P, and S.M.P. Sullivan. 2021. Conservation across aquatic-terrestrial boundaries: linking continental-scale water quality to emergent aquatic insects and declining aerial insectivorous birds. Frontiers in Ecology and Evolution.

Moon, D.L., J.T. Scott, and T.R. Johnson. 2021. Stoichiometric imbalances complicate prediction of phytoplankton biomass in U.S. lakes: Implications for nutrient criteria. Limnology and Oceanography 66(8):2967-2978.

Stetler, J.T., L.B. Knoll, C. T. Driscoll, and K.C. Rose. 2021. Lake browning generates a spatiotemporal mismatch between dissolved organic carbon and limiting nutrients. Limnology and Oceanography Letters 6(4):182-191.

Topp, S.N., T.M. Pavelsky, E.H. Stanley, X. Yang, C.G. Griffin, and M.R.V. Ross. 2021. Multi-decadal improvement in US Lake water clarity. Environmental Research Letters 16(5).

Trottier, G., K. Turgeon, F. Verones, D. Boisclair, C. Bulle, and M. Margni. 2021. Empirical characterization factors for life cycle assessment of the impacts of reservoir occupation on macroinvertebrate richness across the United States. Sustainability 13(5): 2701.

Yuan, L.L. 2021. Continental-scale effects of phytoplankton and non-phytoplankton turbidity on macrophyte occurrence in shallow lakes. Aquatic Sciences 83:14.

2020

Fergus, C.E., J.R. Brooks, P.R. Kaufmann, A.T. Herlihy, A.I. Pollard, M.H. Weber, and S.G. Paulsen. 2020. Lake water levels and associated hydrologic characteristics in the conterminous U.S. Journal of The American Water Resources Association. doi.org/10.1111/1752-1688.12817

Papenfus, M., Schaeffer, B., Pollard, A.I. et al. Exploring the potential value of satellite remote sensing to monitor chlorophyll-a for US lakes and reservoirs. Environ Monit Assess 192, 808 (2020). https://doi.org/10.1007/s10661-020-08631-5

Peck, D.V., S.G. Paulsen, P.R. Kaufmann, and A.T. Herlihy. 2020. Jewels across the landscape: monitoring and assessing the quality of lakes and reservoirs in the United States. Water Quality – Science, Assessments and Policy. DOI: 10.5772/intechopen.92286

Sodré, E.D.O., A. Langlais-Bourassa, A.I. Pollard, and B.E. Beisner. 2020. Functional and taxonomic biogeography of phytoplankton and zooplankton communities in relation to environmental variation across the contiguous USA. Journal of Plankton Research fbaa002.

Stribling, J.B., and E.W. Leppo. 2020. Relationship of taxonomic error to frequency of observation. PLoS ONE 15(11): e0241933.

2019

Bachmann, R.W., S. Sharma, D.E. Canfield Jr., and V. Lecours. 2019. The distribution and prediction of summer near-surface water temperatures in lakes of the coterminous United States and southern Canada. Geosciences 9(7):296.

Doubek, J.P., C.C. Carey, M. Lavender, A.K. Winegardner, M. Beaulieu, P.T. Kelly, A.I. Pollard, D. Straile, and J.D. Stockwell. 2019. Calanoid copepod zooplankton density is positively associated with water residence time across the continental United States. PLoS ONE 14(1): e0209567. doi.org/10.1371/journal.pone.0209567

Griffiths, K., A.K. Winegardner, B.E. Beisner, and I. Gregory-Eaves. 2019. Cladoceran assemblage changes across the Eastern United States as recorded in the sediments from the 2007 National Lakes Assessment, USA. Ecological Indicators 96:368-382. doi.org/10.1016/j.ecolind.2018.08.061

King, K., K.S. Cheruvelil, and A. Pollard. 2019. Drivers and spatial structure of abiotic and biotic properties of lakes, wetlands, and streams at the national scale. Ecological Applications e01957. doi:10.1002/eap.1957

Nojavan, F.A., B.J. Kreakie, J.W. Hollister, and S.S. Qian. 2019. Rethinking the lake trophic state index. PeerJ 7:e7936.

Patrick, C.J., and L.L. Yuan. 2019. The challenges that spatial context present for synthesizing community ecology across scales. Oikos 128(3):297-308.

Ruzycki, E., J. Henneck, W. Bartsch, and R.P. Axler. 2019. Assessing acid‐sensitive lakes in the Superior National Forest. NRRI Technical Report; NRRI/TR-2019/26. University of Minnesota Duluth.

Scott, J.T., M.J. McCarthy, and H.W. Paerl. 2019. Nitrogen transformations differentially affect nutrient-limited primary production in lakes of varying trophic state. Limnology and Oceanography Letters 4(4):96-104. doi.org/10.1002/lol2.10109

Yuan, L.L., and A.I. Pollard. 2019. Combining national and state data improves predictions of microcystin concentration. Harmful Algae 84:75-83. https://doi.org/10.1016/j.hal.2019.02.009

2018

Beaver, J.R., T.R. Renicker, C.E. Tausz, and B.T. Vitanye. 2018. Distribution of six taxa in the family Bosminidae Baird (Crustacea: Branchiopoda: Anomopoda) in the plankton of lakes and reservoirs within the continental United States, including expanded range of the invasive cladoceran Bosmina (Eubosmina) coregoni Baird. Zootaxa 4407(4):506-520.

Beaver, J.R., C.E. Tausz, K.C. Scotese, A.I. Pollard, and R.M. Mitchell. 2018. Environmental factors influencing the quantitative distribution of microcystin and common potentially toxigenic cyanobacteria in U.S. lakes and reservoirs. Harmful Algae 78: 118–128.

Bowen, G.J., A. Putman, J.R. Brooks, D.R. Bowling, E.J. Oerter, and S.P. Good. 2018. Inferring the source of evaporated waters using stable H and O isotopes. Oecologia 187(4):1025-1039.

Hill, R.A., M.H. Weber, R.M. Debbout, S.G. Leibowitz, and A.R. Olsen. 2018. The Lake-Catchment (LakeCat) Dataset: characterizing landscape features for lake basins within the conterminous USA. Freshwater Science 37(2):208-221.

Leech, D.M, A.I. Pollard, S.G. Labou, and S.E. Hampton. 2018. Fewer blue lakes and more murky lakes across the Continental U.S.: Implications for planktonic food webs. Limnology and Oceanography.

Lin, S., L.N. Novitski, J. Qi, and R.J. Stevenson. 2018. Landsat TM/ETM+ and machine-learning algorithms for limnological studies and algal bloom management of inland lakes. Journal of Applied Remote Sensing 12(2):26003. DOI: 10.1117/1.JRS.12.026003

Pollard, A.I., S.E. Hampton, and D.M. Leech. 2018. The promise and potential of continental-scale limnology using the U.S. Environmental Protection Agency’s National Lakes Assessment. Limnology and Oceanography Bulletin 27(2): 36-41.

Yuan, L.L., and A.I. Pollard. 2018. Changes in the relationship between zooplankton and phytoplankton biomasses across a eutrophication gradient. Limnology and Oceanography 63:2493-2507.

2017

Crane, J.L. 2017. Ambient sediment quality conditions in Minnesota lakes, USA: Effects of watershed parameters and aquatic health implications. Science of the Total Environment. 607-608:1320-1338.

Lapierre, J.-F., D.A. Seekell, C.T. Filstrup, S.M. Collins, C. Emi Fergus, P.A. Soranno, and K.S. Cheruvelil. 2017. Continental-scale variation in controls of summer CO₂ in United States lakes. Journal of Geophysical Research Biogeosciences 122:875-885. doi 10.1002/2016JG003525.

Marion, J.W., F. Zhang, D. Cutting, and J. Lee. 2017. Associations between county-level land cover classes and cyanobacteria blooms in the United States. Ecological Engineering 108:556-563.

Taranu, Z.E., I. Gregory-Eaves, R.J. Steele, M. Beaulieu, and P. Legendre. 2017. Predicting microcystin concentrations in lakes and reservoirs at a continental scale: A new framework for modelling an important health risk factor. Global Ecology and Biogeography 26:625-637.

Yuan, L.L., and A.I. Pollard. 2017. Using national-scale data to develop nutrient-microcystin relationships that guide management decisions. Environmental Science & Technology 51:6972-6980.

2016

Beisner, B.E., and C.C. Carey. 2016. Lake Name or Name Lake? The etymology of lake nomenclature in the United States. Freshwater Biology 61(9):1601-1609.

Hollister, J.W., and B.J. Kreakie. 2016. Associations between chlorophyll a and various microcystin-LR health advisory concentrations. F1000Research 5:151 10.12688/f1000research.7955.2

Hollister, J.W., W.B. Milstead, and B.J. Kreakie. 2016. Modeling lake trophic state: A random forest approach. Ecosphere 7:3 10.1002/ecs2.1321

Loftin, K.A., J.L. Graham, E.D. Hilborn, S.C. Lehmann, M.T. Meyer, J.E. Dietze, and C.B. Griffith. 2016. Cyanotoxins in inland lakes of the United States: Occurrence and potential recreational health risks in the EPA National Lakes Assessment 2007. Harmful Algae 56:77-90

Stoddard, J.L., J. Van Sickle, A.T. Herlihy, J. Brahney, S. Paulsen, D.V. Peck, R. Mitchell, and A.I. Pollard. 2016. Continental-scale increase in lake and stream phosphorus: are oligotrophic systems disappearing in the United States? Environmental Science and Technology 50(7):3409-3415. doi:10.1021/acs.est.5b05950

2015

Doubek, J.P., C.C. Carey, and B.J. Cardinale. 2015. Anthropogenic land use is associated with N-fixing cyanobacterial dominance in lakes across the continental United States. Aquatic Sciences 77:681-694.

Ferrey, M.L., S. Heiskary, R. Grace, M.C. Hamilton, and A. Lueck. 2015. Pharmaceuticals and other anthropogenic tracers in surface water: A randomized survey of 50 Minnesota lakes. Environmental Toxicology and Chemistry 34(11):2475-2488. doi:10.1002/etc.3125.

Knoll, L.B., E.J. Hagenbuch, M.H. Stevens, M.J. Vanni, W.H. Renwick, J.C. Denlinger, R.S. Hale, and M.J. Gonzalez. 2015. Predicting eutrophication status at large spatial scales using landscape and morphometric variables. Inland Waters 5(3):202-214.

Read, E.K., V.P. Patil, S.K. Oliver, A.L. Hetherington, J.A. Brentrup, J.A. Zwart, K.M. Winters, J.R. Corman, E.R. Nodine, R.I. Woolway, H.A. Dugan, A. Jaimes, A.B. Santoso, G.S. Hong, L.A. Winslow, P.C. Hanson, and K.C. Weathers. 2015. The importance of lake-specific characteristics for water quality across the continental United States. Ecological Applications 25(4):943-955.

Yuan, L.L., and A.I. Pollard. 2015. Classifying lakes to quantify relationships between epilimnetic chlorophyll a and hypoxia. Environmental Management 55(3):578-587.

Yuan, L.L., and A.I. Pollard. 2015. Deriving nutrient targets to prevent excessive cyanobacterial densities in U.S. lakes and reservoirs. Freshwater Biology 60(9):1901-1916. doi:10.1111/fwb.12620

Zwart, J.A., C.T. Solomon, and S.E. Jones. 2015. Phytoplankton traits predict ecosystem function in a global set of lakes. Ecology 96(8):2257-2264.

2014

Beaver, J.R., E.E. Manis, K.A. Loftin, J.L. Graham, A.I. Pollard, and R.M. Mitchell. 2014. Land use patterns, ecoregion, and microcystin relationships in U.S. lakes and reservoirs: A preliminary evaluation. Harmful Algae 36:57-62.

Brooks, J.R., J.J. Gibson, S.J. Birks, M.H. Weber, K.D. Rodecap, and J.L. Stoddard. 2014. Stable isotope estimates of evaporation: inflow and water residence time for lakes across the United States as a tool for national lake water quality assessments. Limnology and Oceanography 59(6):2150-2165.

Heiskary, S. M. Lindon, and J. Anderson. 2014. Summary of microcystin concentrations in Minnesota lakes. Lake and Reservoir Management 30(3):268-272.

Kaufmann, P.R., R.M. Hughes, J. Van Sickle, T.R. Whittier, C.W. Seeliger, and S.G. Paulsen. 2014. Lakeshore and littoral physical habitat structure: A field survey method and its precision. Lake and Reservoir Management 30(2):157-176.

Kaufmann, P.R., R.M. Hughes, T.R. Whittier, S.A. Bryce, and S.G. Paulsen. 2014. Relevance of lake physical habitat assessment indices to fish and riparian birds. Lake and Reservoir Management 30(2):177-191.

Kaufmann, P.R., D.V. Peck, S.G. Paulsen, C.W. Seeliger, R.M. Hughes, T.R. Whittier, and N.C. Kamman. 2014. Lakeshore and littoral physical habitat structure in a national lakes assessment. Lake and Reservoir Management 30(2):192-215.

Rigoisi, A., C.C. Carey, B.W. Ibelings, and J.D. Brookes. 2014. The interaction between climate warming and eutrophication to promote cyanobacteria is dependent on trophic state and varies among taxa. Limnology and Oceanography 59(1):99-114.

Yuan, L.L., and A.I. Pollard. 2014. Classifying lakes to improve precision of nutrient–chlorophyll relationships. Freshwater Science 33(4):1184-1194.

Yuan, L.L., A.I. Pollard, S. Pather, J.L. Oliver, and L. D’Anglada. 2014. Managing microcystin: identifying national-scale thresholds for total nitrogen and chlorophyll a. Freshwater Biology 59(9):1970-1981.

Zimmerman, E.K., and B.J. Cardinale. 2014. Is the relationship between algal diversity and biomass in North American lakes consistent with biodiversity experiments? Oikos 124(3):267-278.

2013

Beaulieu, M., F.R. Pick, and I. Gregory-Eaves. 2013. Nutrients and water temperature are significant predictors of cyanobacterial biomass in a 1147 lakes dataset. Limnology and Oceanography 58:1736-1746.

Herlihy, A.T., N.C. Kamman, J.C. Sifneos, D. Charles, M.D. Enache, and R.J. Stevenson. 2013. Using multiple approaches to develop nutrient criteria for lakes in the conterminous USA. Freshwater Science 32(2):367-384.

Milstead, W.B., J.W. Hollister, R.B. Moore, and H.A. Walker. 2013. Estimating summer nutrient concentrations in northeastern lakes from SPARROW load predictions and modeled hydraulic residence time. PLoS ONE 8(11):e81457 10.1371/journal.pone.0081457

Peck, D.V., A.R. Olsen, M.H. Weber, S.G. Paulsen, C. Peterson, and S.M. Holdsworth. 2013. Survey design and extent estimates for the National Lakes Assessment. Freshwater Science 32(4):1231-1245.

Stahl, L.L., B.D. Snyder, A.R. Olsen, and L.S. Walters. 2013. A national probabilistic study of polybrominated diphenyl ethers in fish from US lakes and reservoirs. Environmental Monitoring and Assessment 185(12):10351-10364.

Van Sickle, J. 2013. Estimating the risks of multiple, covarying stressors in the National Lakes Assessment. Freshwater Science 32(1):204-216.

2011

Hollister, J.W., W.B. Milstead, and M.A. Urrutia. 2011. Predicting maximum lake depth from surrounding topography. PLoS ONE 6(9):e25764 10.1371/journal.pone.0025764

2002

Whittier, T.R., S.G. Paulsen, D.P. Larsen, S.A. Peterson, A.T. Herlihy, and P.R. Kaufmann. 2002. Indicators of ecological stress and their extent in the population of Northeastern lakes: a regional-scale assessment. Bioscience 52(3):235-247.

Rivers and Streams

2025

Blocksom, K., Flotemersch, J., Ferriby, H., Rabon, B., & Chestnut, D. (2025). Intra-annual and Ecoregional differences in physico-chemical data between Blackwater and non-blackwater streams in the coastal plains of South Carolina. Frontiers in Water, 7. https://doi.org/10.3389/frwa.2025.1540456

2024

Flotemersch, J. E., Blocksom, K. A., Herlihy, A. T., Kaufmann, P. R., Mitchell, R. M., & Peck, D. V. (2024). Distribution and characteristics of blackwater rivers and streams of the contiguous United States. Water Resources Research, 60(2), e2023WR035529. https://doi.org/10.1029/2023WR035529

Jiajia Lin, Jana E Compton, Robert D Sabo, Alan T Herlihy, Ryan A Hill, Marc H Weber, J Renée Brooks, Steve G Paulsen, John L Stoddard, The changing nitrogen landscape of United States streams: Declining deposition and increasing organic nitrogen, PNAS Nexus, Volume 3, Issue 1, January 2024, pgad362, https://doi.org/10.1093/pnasnexus/pgad362

Kaufmann, P. R., Carlisle, D. M., Faustini, J. M., Weber, M. H., Herlihy, A. T., Hill, R. A., ... & Paulsen, S. G. (2024). Quantifying form resistance is essential for estimating summer low and bankfull flow from stream survey channel morphology. Geomorphology, 109360.

Maués-Silva, R., Oliveira-Junior, J. M. B., da Cruz, G. M., & Brasil, L. S. (2024). Evaluation of the environmental quality monitoring protocol for Amazonian streams: a systematic review. Ambiente e Agua-An Interdisciplinary Journal of Applied Science, 19, 1-14.

Miess, S., & Dzialowski, A. R. (2024). Salt Belt Index (SBI): A biotic index for streams within the North American “salt belt,” with proposed baseline chloride thresholds. Science of The Total Environment, 173726.

Moi, D., Kaufmann, P., Riato, L., Romero, G., Kratina, P., Teixeira de Mello, F. and Hughes, R. (2024), Habitat Diversity Mitigates the Impacts of Human Pressure on Stream Biodiversity. Global Change Biology, 30: e17534. https://doi.org/10.1111/gcb.17534

Riato, L., Stoddard, J. L., Herlihy, A. T., & Blocksom, K. A. (2024). Reduced count size can provide a robust and more efficient diatom assessment of environmental conditions. Journal of Applied Ecology.

Smucker, N.J., E.M. Pilgrim, C.T. Nietch, L. Gains-Germain, C. Carpenter, J.A. Darling, L.L. Yuan, R.M. Mitchell, A.I. Pollard. (2024). Using DNA metabarcoding to characterize national scale diatom-environment relationships and to develop indicators in streams and rivers of the United States. Science of The Total Environment. 939. 173502. https://doi.org/10.1016/j.scitotenv.2024.173502

Van Gray, J. B., & Ayayee, P. (2024). Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization. Environmental Microbiology, 26(5), e16628.

Yuan, L.L., D.M. Carlisle, R.M. Mitchell, A.I. Pollard. (2024). Using models of local environmental conditions for biological assessment. Freshwater Science. 43. https://doi.org/10.1086/731770

Yuan, L. L., R. M. Mitchell, E. Pilgrim, Smucker, Nathan. (2024). Inferences based on diatom compositions improve estimates of nutrient concentrations in streams. Science of The Total Environment. 952. 176032. https://doi.org/10.1016/j.scitotenv.2024.176032

2023

Barbo, Nadia, T. Stoiber, O.V. Naidenko, D.Q. Andrews., 2023. Locally caught freshwater fish across the United States are likely a significant source of exposure to PFOS and other perfluorinated compounds. Environmental Research. 220, 115165.

Chen, Kai, Stephen R. Midway, Brandon K. Peoples, Beixin Wang, and Julian D. Olden. 2023. “ Shifting Taxonomic and Functional Community Composition of Rivers under Land Use Change.” Ecology 104(11): e4155. https://doi.org/10.1002/ecy.4155

De Laender, F., Carpentier, C., Carletti, T., Song, C., Rumschlag, S. L., Mahon, M. B., ... & Barabás, G. (2023). Mean species responses predict effects of environmental change on coexistence. Ecology Letters.

Doyle, Jessie M., et al. "Random forest models to estimate bankfull and low flow channel widths and depths across the conterminous United States." JAWRA Journal of the American Water Resources Association (2023).

Fergus, C. E., Brooks, J. R., Kaufmann, P. R., Herlihy, A. T., Hill, R. A., Mitchell, R. M., & Ringold, P. (2023). Disentangling natural and anthropogenic effects on benthic macroinvertebrate assemblages in western US streams. Ecosphere, 14(11), e4688.

Hughes, R. M., Herlihy, A. T., Comeleo, R., Peck, D. V., Mitchell, R. M., & Paulsen, S. G. 2023. Patterns in and predictors of stream and river macroinvertebrate genera and fish species richness across the conterminous USA. Knowledge & Management of Aquatic Ecosystems, (424), 19.

Kaufmann, P. R., Carlisle, D. M., Faustini, J. M., Weber, M. H., Herlihy, A. T., Hill, R. A., & Paulsen, S. G. Estimating Bankfull and Base Flows from Stream Survey Channel Morphology. Available at SSRN 4569262.

Kopp, D., Stoddard, J.L., Hill, R., Doyle, J., Kaufmann, P.R., Herlihy, A., Paulsen, S.G. (2023). Joint species distribution models reveal taxon-specific sensitivities to potential anthropogenic alteration. Freshwater Science 42(3) September2023. https://doi.org/10.1086/726283

Lassiter, M. G., Lin, J., Compton, J. E., Phelan, J., Sabo, R. D., Stoddard, J. L., ... & Greaver, T. L. (2023). Shifts in the composition of nitrogen deposition in the conterminous United States are discernable in stream chemistry. Science of the Total Environment, 881, 163409. https://doi.org/10.1016/j.scitotenv.2023.163409

Lin, J., Compton, J. E., Sabo, R. D., Herlihy, A. T., Hill, R. A., Weber, M. H., ... & Stoddard, J. L. (2023). The changing nitrogen landscape of US streams: Declining deposition and increasing organic nitrogen. PNAS nexus, pgad362.

Rumschlag, S. L., Mahon, M. B., Jones, D. K., Battaglin, W., Behrens, J., Bernhardt, E. S., ... & Rohr, J. R. (2023). Density declines, richness increases, and composition shifts in stream macroinvertebrates. Science Advances, 9(18), eadf4896.

Stahl, L.L., Snyder, B.D., McCarty, H.B., Kincaid, T.M., Olsen, A.R., Cohen, T.R., Healey, J.C. 2023. Contaminants in fish from U.S. rivers: Probability-based national assessments. Science of the Total Environment 861 (2023), 160557.

Sullivan, S. P., Wisseman, R. W., & Pfeiffer, J. (2023). An argument in support of the development of regionalized standard taxonomic efforts for benthic Macroinvertebrate-Based monitoring. Ecological Indicators, 149, 110184.

Yuan, Lester L., R.M. Mitchell, A.I. Pollard, C.T. Nietch, E.M. Pilgrim, and N.J. Smucker 2023. Understanding the effects of phosphorus on diatom richness in rivers and streams using taxon-environment relationships. Freshwater Biology 00:1-14. DOI: 10.1111/fwb.14040.

2022

Carlisle, D. M., Spaulding, S. A., Tyree, M. A., Schulte, N. O., Lee, S. S., Mitchell, R. M., & Pollard, A. A. (2022). A web-based tool for assessing the condition of benthic diatom assemblages in streams and rivers of the conterminous United States. Ecological Indicators, 135, 108513.

Feio, M. J., Hughes, R. M., Serra, S. R., Nichols, S. J., Kefford, B. J., Lintermans, M., Sharma, S. 2023. Fish and macroinvertebrate assemblages reveal extensive degradation of the world's rivers. Global Change Biology, 29(2), 355-374.

Herlihy, A. T., Hughes, R. M., & Gerth, W. J. 2022. Longitudinal patterns in riverine ecology within and among seven Pacific Northwest rivers: Implications for river research, monitoring and management. River Research and Applications, 38(3), 548-560.

Kaufmann, P.R., Hughes, R.M., Paulsen, S.G., Peck, D.V., Seeliger, C.W., Weber, M.H., Mitchell, R.M., 2022. Physical habitat in conterminous US streams and rivers, Part 1: Geoclimatic controls and anthropogenic alteration. Ecol. Indic., 141 109046.

Kaufmann, P.R., Hughes, R.M., Paulsen, S.G., Peck, D.V., Seeliger, C.W., Kincaid, T., Mitchell, R.M., 2022. Physical habitat in conterminous US streams and rivers, part 2: A quantitative assessment of habitat condition. Ecol. Indic. 141, 109047.

Riato, L., Hill, R.A., Herlihy, A.T., Peck, D.V., Kaufmann, P.R., Stoddard, J.L., Paulsen, S.G. 2022. Genus-level, trait-based multimetric diatom indices for assessing the ecological condition of rivers and streams across the conterminous United States. Ecol. Indic. 141, 109131.

Saraiva, S.O., Rutherfurd, I.D., Kaufmann, P.R., Leal, C.G., Macedo, D.R., Pompeu, P.S. 2022. Wood stock in neotropical streams: Quantifying and comparing instream wood among biomes and regions. PLoS ONE 17(10): e0275464.

Saraiva, S.O., Kaufmann, P.R., Rutherfurd, I., Leal, C.G., Leitão, R.P., Macedo, D.R., Pompeu, P.S. 2022. Wood predictors in neotropical streams: assessing the effects of regional and local controls in Amazon and Cerrado catchments. Earth Surface Processes and Landforms. 2022-1-18.

2021

Brooks, J.R., J.E. Compton, J. Lin, A.T. Herlihy, A.M. Nahlik, W. Rugh, and M. Weber. 2021. 15N of Chironomidae: An index of nitrogen sources and processing within watersheds for national aquatic monitoring programs. Science of the Total Environment 813:151867. doi: 10.1016/j.scitotenv.2021.151867.

Feio, M.J.; Hughes, R.M.; Callisto, M.; Nichols, S.J.; Odume, O.N.; Quintella, B.R.; Kuemmerlen, M.; Aguiar, F.C.; Almeida, S.F.P.; Alonso-EguíaLis, P.; Arimoro, F.O.; Dyer, F.J.; Harding, J.S.; Jang, S.; Kaufmann, P.R.; Lee, S.; Li, J.; Macedo, D.R.; Mendes, A.; Mercado-Silva, N.; Monk, W.; Nakamura, K.; Ndiritu, G.G.; Ogden, R.; Peat, M.; Reynoldson, T.B.; Rios-Touma, B.; Segurado, P.; Yates, A.G. 2021. The Biological Assessment and Rehabilitation of the World’s Rivers: An Overview. Water 13, 371.

Hughes, R.M., A.T. Herlihy, and D.V. Peck. 2021. Sampling efforts for estimating fish species richness in western USA river sites. Limnologica 87:125859.

Hughes, R. M., Zeigler, M., Stringer, S., Linam, G. W., Flotemersch, J., Jessup, B., ... & Barrios, K. 2022. Biological assessment of western USA sandy bottom rivers based on modeling historical and current fish and macroinvertebrate data. River research and applications, 38(4), 639-656.

Lin, J., J. Compton, R.A. Hill, A.T. Herlihy, R. Sabo, J.R. Brooks, M.H. Weber, B. Pickard, S.G. Paulsen, and J.L. Stoddard. 2021. Context is everything: interacting inputs and landscape characteristics control stream nitrogen. Environmental Science & Technology 55:7890-7899. doi: 10.1021/acs.est.0c07102.

Lomnicky, G.A., R.M. Hughes, D.V. Peck, and P.L. Ringold. 2021. Correspondence between a recreational fishery index and ecological condition for U.S.A. streams and rivers. Fisheries Research 233:105749.

Mejia, F.H., Conner, J.M., Kaufmann, P.R., Torgersen, C.E., Berntsen, E.K., and Andersen, T.K. 2021. Integrating regional and local monitoring data and assessment tools to evaluate habitat conditions and inform river restoration. Ecol. Indic. 131, 108213.

Manning, D.W.P, S.M.P. Sullivan. 2021. Conservation across aquatic-terrestrial boundaries: linking continental-scale water quality to emergent aquatic insects and declining aerial insectivorous birds. Frontiers in Ecology and Evolution.

2020

Herlihy, A.T., J.C. Sifneos, R.M. Hughes, D.V. Peck, and R.M. Mitchell. 2020. The relation of lotic fish and benthic macroinvertebrate condition indices to environmental factors across the conterminous USA. Ecological Indicators 112:105958.

Larson, D.C., M. Helstab, M.F. Docker, B. Bangs, and B.J. Clemens. 2020. Landlocked Pacific Lamprey Entosphenus tridentatus in the Middle Fork Willamette River, Oregon. Environmental Biology of Fishes 103: 291–298.

Paulsen, S.G., D.V. Peck, P.R. Kaufmann, and A.T. Herlihy. 2020. Rivers and streams: upgrading monitoring of the nation’s freshwater resources - meeting the spirit of the Clean Water Act. Water Quality – Science, Assessments and Policy. DOI: 10.5772/intechopen.92823.

Riato, L., S.G. Leibowitz, and M.H. Weber. 2020. The use of multiscale stressors with biological condition assessments: A framework to advance the assessment and management of streams. Science of the Total Environment 737:139699.

Stribling, J.B., and E.W. Leppo. 2020. Relationship of taxonomic error to frequency of observation. PLoS ONE 15(11): e0241933.

2019

Lee, S. S., Bishop, I. W., Spaulding, S. A., Mitchell, R. M., & Yuan, L. L. (2019). Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets. Ecological Indicators, 102, 166-174.

Patrick, C.J., and L.L. Yuan. 2019. The challenges that spatial context present for synthesizing community ecology across scales. Oikos 128(3):297-308.

Sprague, L.A., R.M. Mitchell, A.I. Pollard, and J.A. Falcone. 2019. Assessing water-quality changes in US rivers at multiple geographic scales using results from probabilistic and targeted monitoring. Environmental Monitoring and Assessment 191:348. https://doi.org/10.1007/s10661-019-7481-5

2018

Bellmore, R.A., J.E. Compton, J.R. Brooks, E.W. Fox, R.A. Hill, D.J. Sobota, D.J. Thornbrugh, and M.H. Weber. 2018. Nitrogen inputs drive nitrogen concentrations in US streams and rivers during summer low flow conditions. Science of the Total Environment 639:1349-1359.

Huerta, B., S. Rodriguez-Mozaz, J. Lazorchak, D. Barcelo, A. Batt, J. Wathen, and L. Stahl. 2018. Presence of pharmaceuticals in fish collected from urban rivers in the U.S. EPA 2008-2009 National Rivers and Streams Assessment. Science of the Total Environment 634:542-549. doi: 10.1016/j.scitotenv.2018.03.387.

Leal, C. G., J. Barlow, T. Gardner, R.M. Hughes, R.P. Leitão, R. MacNally, P.R. Kaufmann, S.F.B. Ferraz, J. Zuanon, F.R. de Paula, J. Ferreira, J.R. Thomson, G.D. Lennox, E.P. Dary, C.P. Röpke, C. P. and P.S. Pompeu. 2018. Is environmental legislation conserving tropical stream faunas? A large-scale assessment of local, riparian and catchment-scale influences on Amazonian stream fish. J. Appl. Ecol. 55:1312- 1326.

Leitão, R.P., J. Zuanon, C.G. Leal, P.S. Pompeu, T. Gardner, J. Barlow, R.M. Hughes, P.R. Kaufmann, J. Ferreira, D. Kasper, S. Villéger, D. Mouillot. 2018. Disentangling the multiple effects of land use on the functional structure of fish assemblages in small Amazon streams. Ecography 41: 219–232. doi:10.1111/ecog.02845.

Macedo, DR., R.M. Hughes, P.R. Kaufmann, M. Callisto. 2018. Development and validation of an environmental fragility index (EFI) for the neotropical savannah biome. Science of the Total Environment. 635:1267-1279.

Thornbrugh, D.J., S.G. Leibowitz, R.A. Hill, M.H. Weber, Z.C. Johnson, A.R. Olsen, J.E. Flotermersch, J.L. Stoddard, and D.V. Peck. 2018. Mapping watershed integrity for the conterminous United States. Ecological Indicators 85:1133-1148.

2017

Batt, A.L., J.B. Wathen, J.M. Lazorchak, A.R. Olsen, and T.M. Kincaid. 2017. Statistical survey of persistent organic pollutants: risk estimations to humans and wildlife through consumption of fish from U.S. rivers. Environmental Science and Technology 51(5):3021-3031. doi: 10.1021/acs.est.6b05162

Carlisle, D.M., T.E. Grantham, K. Eng, and D.M. Wolock. 2017. Biological relevance of streamflow metrics: regional and national perspectives. Freshwater Science 36(4):927-940.

Hill, B.H., C.M. Elonen, A.T. Herlihy, T.M. Jicha, and R.M. Mitchell. 2017. A synoptic survey of microbial respiration, organic matter decomposition, and carbon efflux in U.S. streams and rivers. Limnology and Oceanography 62(S1):S147-S159. doi:10.1002/lno.10583

Hill, R.A., E.W. Fox, S.G. Leibowitz, A.R. Olsen, D.J. Thornbrugh, and M.H. Weber. 2017. Predictive mapping of the biotic condition of conterminous U.S. rivers and streams. Ecological Applications 27(8):2397-2415.

Van Metre, P.C., D.A. Alvarez, B.J. Mahler, L. Nowell, M. Sandstrom, and P. Moran. 2017. Complex mixtures of pesticides in midwest U.S. streams indicated by POCIS time-integrating samplers. Environmental Pollution 220:431-440.

2016

Batt, A.L., T.M. Kincaid, M.S. Kostich, J.M. Lazorchak, and A.R. Olsen. 2016. Evaluating the extent of pharmaceuticals in surface waters of the United States using a national-scale rivers and streams assessment survey. Environmental Toxicology and Chemistry 35(4):874-881. doi:10.1002/etc.3161.

Hill. R.A., M.H. Weber, S.G. Leibowitz, A.R. Olsen, and D.J. Thornbrugh. 2016. The Stream‐Catchment (StreamCat) Dataset: A Database of Watershed Metrics for the Conterminous United States. Journal of the American Water Resources Association 52(1):120-128.

Hubler, S., D.D. Huff, P. Edwards, and Y. Pan. 2016. The Biological Sediment Tolerance Index: Assessing fine sediments conditions in Oregon streams using macroinvertebrates. Ecological Indicators 67:132-145.

Leal, C.G., P.S. Pompeu, T. Gardner, R.P. Leitão, R.M. Hughes, P.R. Kaufmann, J. Zuanon, F.R. de Paula, S. Ferraz, J.R. Thomson, R. MacNally, J. Ferreira, J. Barlow. 2016. Multi-scale assessment of human-induced changes to Amazonian instream habitats. Landscape Ecology 31:1725-1745. DOI 10.1007/s10980-016-0358-x

Omernik, J., S. Paulsen, G. Griffith, and M. Weber. 2016. Regional patterns of total nitrogen concentrations in the National Rivers and Streams Assessment. Journal of Soil and Water Conservation 71(3): 167-181.

Van Metre, P.C., J.W. Frey, M. Musgrove, N. Nakagaki, S. Qi, B.J. Mahler, M.E. Wieczorek, and D.T. Button. 2016. High nitrate concentrations in some midwest United States streams in 2013 after the 2012 drought. Journal of Environmental Quality 45:1696–1704.

2015

Hughes, R.M., A.T. Herlihy, and J.C. Sifneos. 2015. Predicting aquatic vertebrate assemblages from environmental variables at three multistate geographic extents of the western USA. Ecological Indicators 57:546-556. doi: 10.1016/j.ecolind.2015.04.044.

Scott, T. 2015. Does collaboration make any difference? Linking collaborative governance to environmental outcomes. Journal of Policy Analysis and Management 34(3):537-566. doi:10.1002/pam.21836.

Wathen, J.B., J.M. Lazorchak, A.R. Olsen, and A. Batt. 2015. A national statistical survey assessment of mercury concentrations in fillets of fish collected in the U.S. EPA national rivers and streams assessment of the continental USA. Chemosphere 122:52-61. doi:10.1016/j.chemosphere.2014.11.005.

2014

Flotemersch, J.E., S. North, and K.A. Blocksom. 2014. Evaluation of an alternate method for sampling benthic macroinvertebrates in low-gradient streams sampled as part of the National Rivers and Streams Assessment. Environmental Monitoring and Assessment 186:949-959.

Hill, B.H., R.K. Kolka, F.H. McCormick, and M.A. Starry. 2014. A synoptic survey of ecosystem services from headwater catchments in the United States. Ecosystem Services 7:106-115.

Jessup, B.K., P.R. Kaufmann, F. John, L.S. Guevara, and S. Joseph. 2014. Bedded sediment conditions and macroinvertebrate responses in New Mexico streams: A first step in establishing sediment criteria. Journal of the American Water Resources Association 50(6):1558-1574. doi:10.1111/jawr.12224.

Kaufmann, P.R., R.M. Hughes, J. Van Sickle, T.R. Whittier, C.W. Seeliger, and S.G. Paulsen. 2014a. Lakeshore and littoral habitat structure: a field survey method and its precision. Lake & Reservoir Management 30:157-176.

Kaufmann, P.R., R.M. Hughes, T.R. Whittier, S.A. Bryce, and S.G. Paulsen. 2014b. Relevance of lake physical habitat assessment indices to fish and riparian birds. Lake & Reservoir Management 30:177-191.

Kaufmann, P.R., D.V. Peck, S.G. Paulsen, C.W. Seeliger, R.M. Hughes, T.R. Whittier, and N.C. Kamman. 2014c. Lakeshore and littoral physical habitat structure in a national lakes assessment. Lake & Reservoir Management 30:192-215.

Wilkerson, G.V., D.R. Kandel, L.A. Perg, W.E. Dietrich, P.R. Wilcock, and M.R. Whiles. 2014. Continental-scale relationship between bankfull width and drainage area for single-thread alluvial channels. Water Resources Research 50(2):919-936. doi:10.1002/2013WR013916.

2012

Hill, B.H., C.M. Elonen, L.R. Seifert, A.A. May, and E. Tarquinio. 2012. Microbial enzyme stoichiometry and nutrient limitation in US streams and rivers. Ecological Indicators 18:540-551.

Kaufmann, P.R., and J.M. Faustini. 2012. Simple measures of channel habitat complexity predict transient hydraulic storage in streams. In a special issue: The Importance of Habitat Complexity in Waterscapes Hydrobiologia 685(1):69-95.

Pan, Y., R.M Hughes, A.T. Herlihy, and P.R. Kaufmann. 2012. Non-wadeable river bioassessment: spatial variation of benthic diatom assemblages in Pacific Northwest rivers, USA. Hydrobiologia 684(1):241-260.

2011

Hill, B.H., and D.W. Bolgrien. 2011. Nitrogen removal by streams and rivers of the Upper Mississippi River basin. Biogeochemistry 102:183-194. DOI 10.1007/s10533-010-9431-8.

Hill, B.H., D.W. Bolgrien, A.T. Herlihy, T.M. Jicha, and T.R. Angradi. 2011. Synoptic survey of nitrogen and phosphorus in tributary streams and great rivers of the Upper Mississippi, Missouri, and Ohio River Basins. Water, Air, and Soil Pollution 216:605–619. DOI 10.1007/s11270-010-0556-0.

Hughes, R.M., P.R. Kaufmann, and M. Weber. 2011. National and regional comparisons between Strahler order and stream size. Journal of the North American Benthological Society 30(1):103-121.

2010

Bryce, S.A., G.A. Lomnicky, and P.R. Kaufmann. 2010. Protecting sediment-sensitive aquatic species in mountain streams through the application of biologically based criteria streambed sediment criteria. Journal of the North American Benthological Society 29(2):657-672.

Hughes, R.M., A.T. Herlihy, and P.R. Kaufmann. 2010. An evaluation of qualitative indices of physical habitat applied to agricultural streams in ten U.S. States. Journal of the American Water Resources Association 46(4):792-806.

Yuan, L.L. 2010. Estimating the effects of excess nutrients on stream invertebrates from observational data. Ecological Applications 20(1):110-125.

2009

Faustini, J.M., P.R. Kaufmann, and A.T. Herlihy. 2009. Downstream variation in bankfull width of wadeable streams across the conterminous United States. Geomorphology 108:292-311.

Kaufmann, P.R., D.P. Larsen, and J.M. Faustini. 2009. Bed stability and sedimentation associated with human disturbances in Pacific Northwest streams. Journal of the American Water Resources Association 45(2):434-459.

2008

Kaufmann, P.R., J.M. Faustini, D.P. Larsen, and M.A. Shirazi. 2008. A roughness-corrected index of relative bed stability for regional stream surveys. Geomorphology 99:150-170.

Olsen, A.R. and D.V. Peck. 2008. Survey design and extent estimates for the Wadeable Streams Assessment. Journal of the North American Benthological Society 27:822-836.

Paulsen, S.G., A. Mayio, D.V. Peck, J.L. Stoddard, E. Tarquinio, S. Holdsworth, J. Van Sickle, L.L. Yuan, C.P. Hawkins, A.T. Herlihy, P.R. Kaufmann, M.T. Barbour, D.P. Larsen, and A.R. Olsen. 2008. Condition of stream ecosystems in the United States: An overview of the first national assessment. Journal of the North American Benthological Society 27(4):812-821.

Stribling, J.B., K.L. Pavlik, S.M. Holdsworth, and E.W. Leppo. 2008. Data quality, performance, and uncertainty in taxonomic identification for biological assessments. Journal of the North American Benthological Society 27(4):906-919. doi: 10.1899/07-175.1.

Yuan, L.L., C.P. Hawkins, and J. Van Sickle. 2008. Effects of regionalization decisions on an O/E index for the US national assessment. Journal of the North American Benthological Society 27(4):892-905.

2007

Faustini, J.M., and P.R. Kaufmann. 2007. Adequacy of visually classified particle count statistics from regional stream habitat surveys. Journal of the American Water Resources Association 43(5):1293-1315.

1999

Kaufmann, P.R., P. Levine, E.G. Robison, C. Seeliger, and D.V. Peck. 1999. Quantifying physical habitat in wadeable streams. EPA 620/R-99/003. Environmental Monitoring and Assessment Program, U.S. Environmental Protection Agency, Corvallis, OR. Search the EPA Archive for this document.