USGS - science for a changing world

USGS Water Resources Applications Software: OTIS

OTIS Applications

This page contains a bibliography of OTIS applications that have been published in the literature. Access to HTML and PDF versions of the publications is provided where possible. Note that access to journal articles may be restricted to site visitors with personal or institutional subscriptions to the specific journals. Access to PDF files () requires Adobe Reader or an alternate PDF viewer.

If you have a published OTIS application that is not on this list, please let us know.

Antweiler, R.C., Writer, J.H., and Murphy, S.F., 2014,
Evaluation of wastewater contaminant transport in surface waters using verified Lagrangian sampling: Science of the Total Environment, v. 470-471, p. 551–558, doi: 10.1016/j.scitotenv.2013.09.079
DOI | PDF

Argerich, A., Martí, E., Sabater, F., Ribot, M., von Schiller, D., and Riera, J.L., 2008,
Combined effects of leaf litter inputs and a flood on nutrient retention in a Mediterranean mountain stream during fall: Limnology and Oceanography, v. 53, no. 2, p. 631-641, doi:10.4319/lo.2008.53.2.0631
DOI | PDF

Argerich, A., Haggerty, R., Martí, E., Sabater, F., and Zarnetske, J., 2011,
Quantification of metabolically active transient storage (MATS) in two reaches with contrasting transient storage and ecosystem respiration: Journal of Geophysical Research, v. 116, G03034, doi:10.1029/2010JG001379
DOI | PDF

Argerich, A.. Martí, E., Sabater, F., Haggerty, R., Ribot, M., 2011,
Influence of transient storage on stream nutrient uptake based on substrata manipulation: Aquatic Sciences, v. 73, no. 3, p. 365-376, doi: 10.1007/s00027-011-0184-9
DOI | PDF

Argerich, A., Martí, E., Sabater, F., and Ribot, M., 2011,
Temporal variation of hydrological exchange and hyporheic biogeochemistry in a headwater stream during autumn: Journal of the North American Benthological Society, v. 30, no. 3, p. 635-652, doi: 10.1899/10-078.1
DOI | PDF

Baker, D.W., and Bledsoe, B.P., and Mueller Price, J., 2012,
Stream nitrate uptake and transient storage over a gradient of geomorphic complexity, north-central Colorado, USA: Hydrological Processes, v. 26, no. 21, p. 3241-3252, doi: 10.1002/hyp.8385
DOI | PDF

Battin, T.J., Kaplan, L.A., Newbold, J.D., and Hansen, C.M., 2003,
Contributions of microbial biofilms to ecosystem processes in stream mesocosms: Nature, v. 426, p. 439-442, doi:10.1038/nature02152
DOI | PDF

Beaulieu, J.J., Arango, C.P., Balz, D.A., and Shuster, W.D., 2013,
Continuous monitoring reveals multiple controls on ecosystem metabolism in a suburban stream: Freshwater Biology, v. 58, no. 5, p. 918-937, doi: 10.1111/fwb.12097
DOI | PDF

Becker, J.F., Endreny, T.A., Robinson, J.D., 2013,
Natural channel design impacts on reach-scale transient storage: Ecological Engineering, v. 57, p. 380-392, doi: 10.1016/j.ecoleng.2013.04.051
DOI | PDF

Benjamin, J.R., Bellmore, J.R., and Watson, G.A., 2016,
Response of ecosystem metabolism to low densities of spawning Chinook Salmon: Freshwater Science, v. 35, no. 3, p. 810-825, doi: 10.1086/686686
DOI | PDF

Bernot, M.J., Tank, J.L., Royer, T.V., and David, M.B., 2006,
Nutrient uptake in streams draining agricultural catchments of the midwestern United States: Freshwater Biology, v. 51, no. 3, p. 499-509, doi:10.1111/j.1365-2427.2006.01508.x
DOI | PDF

Bernot, M.J., Sobota, D.J., Hall, R.O., Mulholland, P.J., et al., 2010,
Inter-regional comparison of land-use effects on stream metabolism: Freshwater Biology, v. 55, no. 9, p. 1874-1890, doi:10.1111/j.1365-2427.2010.02422.x
DOI | PDF

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, doi:10.4319/lo.2004.49.3.0821
DOI | PDF

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, doi:10.1007/s10533-008-9282-8
DOI | PDF

Bott, T.L., Newbold, J.D., and Arscott, D.B., 2006,
Ecosystem metabolism in piedmont streams: Reach geomorphology modulates the influence of riparian vegetation: Ecosystems, v. 9, no. 3, p. 398-421, doi:10.1007/s10021-005-0086-6
DOI | PDF

Bourke, S.A., Cook, P.G, Shanafield, M., Dogramaci, S., Clark, J.F., 2014,
Characterisation of hyporheic exchange in a losing stream using radon-222: Journal of Hydrology, v. 519, p. 94-105, doi: 10.1016/j.jhydrol.2014.06.057
DOI | PDF

Briggs, M.A., Gooseff, M.N., Peterson, B.J., Morkeski, K., Wollheim, W.M., and Hopkinson, C.S., 2010,
Surface and hyporheic transient storage dynamics throughout a coastal stream network: Water Resources Research, v. 46, W06516, doi:10.1029/2009WR008222
DOI | PDF

Chapra, S.C., and Wilcock, R.J., 2000,
Transient storage and gas transfer in lowland stream: Journal of Environmental Engineering, v. 126, no. 8, p. 708-712, doi:10.1061/(ASCE)0733-9372(2000)126:8(708)
DOI | PDF

Choi, J., Hulseapple, S.M., Conklin, M.H., and Harvey, J.W., 1999,
Modeling CO2 degassing and pH in a stream-aquifer system: Journal of Hydrology, v. 209, p. 297-310, doi:10.1016/S0022-1694(98)00093-6
DOI | PDF

Choi, J., Harvey, J.W., and Conklin, M.H., 2000,
Characterizing multiple timescales of stream and storage zone interaction that affect solute fate and transport in streams: Water Resources Research, v. 36, no. 6, p 1511-1518, doi:10.1029/2000WR900051
DOI | PDF

Claessens, L., and Tague, C.L., 2009,
Transport-based method for estimating in-stream nitrogen uptake at ambient concentration from nutrient addition experiments: Limnology and Oceanography Methods, v. 7, p. 811-822
URL | PDF

Claessens, L., Tague, C.L., Groffman, P.M., and Melack, J.M., 2010,
Longitudinal and seasonal variation of stream N uptake in an urbanizing watershed: Effect of organic matter, stream size, transient storage and debris dams: Biogeochemistry, v. 98, p. 45-62, doi:10.1007/s10533-009-9375-z
DOI | PDF

Claessens, L., Tague, C.L., Groffman, P.M., and Melack, J.M., 2010,
Longitudinal assessment of the effect of concentration on stream N uptake rates in an urbanizing watershed: Biogeochemistry, v. 98, p. 63-74, doi:10.1007/s10533-009-9376-y
DOI | PDF

Cozzetto, K., McKnight, D., Nylen, T., and Fountain, A., 2006,
Experimental investigations into processes controlling stream and hyporheic temperatures, Fryxell Basin, Antarctica: Advances in Water Resources, v. 29, no. 2, p. 130-153, doi:10.1016/j.advwatres.2005.04.012
DOI | PDF

Cozzetto, K.D., Bencala, K.E., Gooseff, M.N., and McKnight, D.M., 2013,
The influence of stream thermal regimes and preferential flow paths on hyporheic exchange in a glacial meltwater stream: Water Resources Research, v. 49, p. 5552–5569, doi: 10.1002/wrcr.20410
DOI | PDF

Crenshaw, C.L., Grimm, N.B., Zeglin, L.H., Sheibley, R.W., Dahm, C.N., and Ershall, A.D.P., 2010,
Dissolved inorganic nitrogen dynamics in the hyporheic zone of reference and human-altered southwestern U. S. streams: Fundamental and Applied Limnology / Archiv für Hydrobiologie, v. 176, no. 4, p. 391-405, doi:10.1127/1863-9135/2010/0176-0391
DOI

Crouch, C.M., McKnight, D.M., and Todd, A.S., 2013,
Quantifying sources of increasing zinc from acid rock drainage in an alpine catchment under a changing hydrologic regime: Hydrological Processes, v. 27, no. 5, p 721-733, doi: 10.1002/hyp.9650
DOI | PDF

Cunnings, A., Johnson, E., and Martin, Y., 2016,
Fluvial seed dispersal of riparian trees: transport and depositional processes: Earth Surface Processes and Landforms, v. 41, no. 5, p. 615-625, doi: 10.1002/esp.3850
DOI | PDF

De Smedt, F., Brevis, W., and Debels, P., 2005,
Analytical solution for solute transport resulting from instantaneous injection in streams with transient storage: Journal of Hydrology, v. 315, p. 25-39, doi:10.1016/j.jhydrol.2005.04.002
DOI | PDF

De Smedt, F., 2006,
Analytical solutions for transport of decaying solutes in rivers with transient storage: Journal of Hydrology, v. 330, p. 672-680, doi:10.1016/j.jhydrol.2006.04.042
DOI | PDF

Dewaide, L., Bonniver, I., Rochez, G., and Hallet, V., 2016,
Solute transport in heterogeneous karst systems: Dimensioning and estimation of the transport parameters via multi-sampling tracer-tests modelling using the OTIS (One-dimensional Transport with Inflow and Storage) program: Journal of Hydrology, v. 534, p. 567-578, doi: 10.1016/j.jhydrol.2016.01.049
DOI | PDF

Dodds, W.K., et al., 2008,
Nitrogen cycling and metabolism in the thalweg of a prairie river: Journal of Geophysical Research, v. 113, G04029, doi:10.1029/2008JG000696
DOI | PDF

Duff, J.H., Tesoriero, A.J., Richardson, W.B., Strauss, E.A., and Munn, M.D., 2008,
Whole-stream response to nitrate loading in three streams draining agricultural landscapes: Journal of Environmental Quality, v. 37, no. 3, p. 1133-1144, doi:10.2134/jeq2007.0187
DOI | PDF

Edwardson, K.J., Bowden, W.B., Dahm, C., and Morrice, J., 2003,
The hydraulic characteristics and geochemistry of hyporheic and parafluvial zones in Artic tundra streams, north slope, Alaska: Advances in Water Resources, v. 26, no. 9, p. 907-924, doi:10.1016/S0309-1708(03)00078-2
DOI | PDF

Ensign, S.H., and Doyle, M.W., 2005,
In-channel transient storage and associated nutrient retention: Evidence from experimental manipulations: Limnology and Oceanography, v. 50, no. 6, p. 1740-1751, doi:10.4319/lo.2005.50.6.1740
DOI | PDF

Fabian, M.W., Endreny, T.A., Bottacin-Busolin, A., and Lautz, L.K., 2011,
Seasonal variation in cascade-driven hyporheic exchange, northern Honduras: Hydrological Processes, v. 25, no. 10, p. 1630-1646, doi: 10.1002/hyp.7924
DOI | PDF

Faulkner, B.R., and Campana, M.E., 2007,
Compartmental model of nitrate retention in streams: Water Resources Research, v. 43, W02406, doi:10.1029/2006WR004920
DOI | PDF

Fellows, C.S., Valett, H.M., and Dahm, C.N., 2001,
Whole-stream metabolism in two montane streams: Contribution of the hyporheic zone: Limnology and Oceanography, v. 46, no. 3, p. 523-531
DOI | PDF

Fernald, A.G., Wigington, P.J., and Landers, D.H., 2001,
Transient storage and hyporheic flow along the Willamette River, Oregon: Field measurements and model estimates: Water Resources Research, v. 37, no. 6, p. 1681-1694, doi:10.1029/2000WR900338
DOI | PDF

García, V.J., Gantes, P., Giménez, L., Hegoburu, C., Ferreiro, N., Sabater, F., and Feijoó, C., 2017,
High nutrient retention in chronically nutrient-rich lowland streams: Freshwater science, v. 36, no. 1, p. 26-40, doi: 10.1086/690598
DOI | PDF

Garneau, C., Sauvage, S., Probst, A., and Sánchez-Pérez, J.M., 2015,
Modelling of trace metal transfer in a large river under different hydrological conditions (the Garonne River in southwest France): Ecological Modelling, v. 306, p. 195-204, doi:10.1016/j.ecolmodel.2014.09.011
DOI | PDF

González-Pinzón, R., Ward, A.S., Hatch, C.E., Wlostowski, A.N., Singha, K., Gooseff, M.N., Haggerty, R., Harvey, J.W., Cirpka, O.A., and Brock, J.T., 2015
A field comparison of multiple techniques to quantify groundwater-surface-water interactions: Freshwater Science, v. 34, no. 1, p. 139-160, doi: 10.1086/679738
DOI | PDF

Gooseff, M.N., McKnight, D.M., Lyons, W.B., and Blum, A.E., 2002,
Weathering reactions and hyporheic exchange controls on stream water chemistry in a glacial meltwater stream in the McMurdo Dry Valleys: Water Resources Research, v. 38, no. 12, p. 151-1517, doi:10.1029/2001WR000834
DOI | PDF

Gooseff, M.N., McKnight, D.M., Runkel, R.L., and Vaughn, B.H., 2003,
Determining long time-scale hyporheic zone flow paths in Antarctic streams: Hydrological Processes, v. 17, no. 9, p. 1691-1710, doi: 10.1002/hyp.1210
DOI | PDF

Gooseff, M.N., Wondzell, S.M., Haggerty, R., and Anderson, J., 2003,
Comparing transient storage modeling and residence time distribution (RTD) analysis in geomorphically varied reaches in the Lookout Creek basin, Oregon, USA: Advances in Water Resources, v. 26, no. 9, p. 925-937, doi:10.1016/S0309-1708(03)00105-2
DOI | PDF

Gooseff, M.N., McKnight, D.M., and Runkel, R.L., 2004,
Reach-Scale cation exchange controls on major ion chemistry of an Antarctic glacial meltwater stream: Aquatic Geochemistry, v. 10, p. 221-238, doi:10.1007/s10498-004-2260-4
DOI | PDF

Gooseff, M.N., McKnight, D.M., Runkel, R.L., and Duff, J.H., 2004,
Denitrification and hydrologic transient storage in a glacial meltwater stream, McMurdo Dry Valleys, Antarctica: Limnology and Oceanography, v. 49, no. 5, p. 1884-1895
DOI | PDF

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, no. 5, p. 479-492, doi:10.1016/j.advwatres.2004.11.012
DOI | PDF

Gooseff, M.N., and McGlynn, B.L., 2005,
A stream tracer technique employing ionic tracers and specific conductance data applied to the Maimai catchment, New Zealand: Hydrological Processes, v. 19, no. 13, p. 2491-2506, doi:10.1002/hyp.5685
DOI | PDF

Gooseff, M.N., Briggs, M.A., Bencala, K.E., McGlynn, B.L., Scott, D.T., 2013,
Do transient storage parameters directly scale in longer, combined stream reaches? Reach length dependence of transient storage interpretations: Journal of Hydrology, v. 483, p. 16-25, doi: 10.1016/j.jhydrol.2012.12.046
DOI | PDF

Grant, S.B., Litton-Mueller, R.M., and Ahn, J.H., 2011,
Measuring and modeling the flux of fecal bacteria across the sediment-water interface in a turbulent stream: Water Resources Research, v. 47, W05517, 13 p., doi:10.1029/2010WR009460
DOI | PDF

Gücker, B., and Boëchat, I.G., 2004,
Stream morphology controls ammonium retention in tropical headwaters: Ecology, v. 85, no. 10, p. 2818-2827, doi:10.1890/04-0171
DOI | PDF

Gücker, B., and Pusch, M.T., 2006,
Regulation of nutrient uptake in eutrophic lowland streams: Limnology and Oceanography, v. 51, no. 3, p. 1443-1453, doi:10.4319/lo.2006.51.3.1443
DOI | PDF

Gücker, B., Boëchat, I.G., and Giani, A., 2009,
Impacts of agricultural land use on ecosystem structure and whole-stream metabolism of tropical Cerrado streams: Freshwater Biology, v. 54, no. 10, p. 2069-2085, doi:10.1111/j.1365-2427.2008.02069.x
DOI | PDF

Hall, R.O. Jr., Tank, J.L., Sobota, D.J., Mulholland, P.J., et al., 2009,
Nitrate removal in stream ecosystems measured by 15N addition experiments: Total uptake: Limnology and Oceanography, v. 54, no. 3, p. 653-665
DOI | PDF

Harvey, J.W., and Fuller, C.C., 1998,
Effect of enhanced manganese oxidation in the hyporheic zone on basin-scale geochemical mass balance: Water Resources Research, v. 34, no. 4, p. 623-636, doi:10.1029/97WR03606
DOI | PDF

Harvey, J.W., Conklin, M.H., and Koelsch, R.S., 2003,
Predicting changes in hydrologic retention in an evolving semi-arid alluvial stream: Advances in Water Resources, v. 26, no. 9, p. 939-950, doi:10.1016/S0309-1708(03)00085-X
DOI | PDF

Harvey, J.W., Saiers, J.E., Newlin, J.T., 2005,
Solute transport and storage mechanisms in wetlands of the Everglades, south Florida: Water Resources Research, v. 41, W05009, doi:10.1029/2004WR003507
DOI | PDF

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, doi:10.1016/j.jhydrol.2005.07.024
DOI | PDF

Herrman, K.S., Bouchard, V., Granata, T., Carey, A.E., and Moore, R.H., 2010,
The effect of riparian land use on transport hydraulics in agricultural headwater streams located in northeast Ohio, USA: Hydrological Processes, v. 24, no. 1, p.1-12, doi:10.1002/hyp.7489
DOI | PDF

Hill, B.H., McCormick, F.H., Harvey, B.C., Johnson, S.L., Warren, M.L., and Elonen, C. M., 2010,
Microbial enzyme activity, nutrient uptake and nutrient limitation in forested streams: Freshwater Biology, v. 55, no. 5, p. 1005-1019, doi:10.1111/j.1365-2427.2009.02337.x
DOI | PDF

Hoagland, B., Russo, T.A., Gu, X., Hill, L., Kaye, J., Forsythe, B., and Brantley, S.L., 2017,
Hyporheic zone influences on concentration-discharge relationships in a headwater sandstone stream,: Water Resources Research v. 53, p. 4643-4667, doi: 10.1002/2016WR019717
DOI | PDF

Hünken, A., 2006,
Resuspension of particulate organic matter in sand-bed lowland streams: Archiv fur Hydrobiologie, v. 166, no. 2, p. 169-183, doi:10.1127/0003-9136/2006/0166-0169
DOI

Hünken, A., Mutz, M., 2007,
Field studies on factors affecting very fine and ultra fine particulate organic matter deposition in low-gradient sand-bed streams: Hydrological Processes, v. 21, p. 525-533, doi:10.1002/hyp.6263
DOI | PDF

Jin, H., and Ward, G.M., 2005,
Hydraulic characteristics of a small Coastal Plain stream of the southeastern United States: effects of hydrology and season: Hydrological Processes, v. 19, p. 4147-4160, doi:10.1002/hyp.5878
DOI | PDF

Jin, H.S., White, D., Ramsey, J., Kipphut, G., 2012,
Mixed tracer injection method to measure reaeration coefficients in small streams: Water, Air, & Soil Pollution, v. 223, no. 8, p. 5297-5306, doi: 10.1007/s11270-012-1280-8
DOI | PDF

Jin, H., and Ward, G. M., 2013,
Fine particulate organic matter transport dynamics in a small Coastal Plain stream: influence of hydrology and channel morphology: Aquatic Sciences, v. 75, no. 4, p. 483-492, doi: 10.1007/s00027-013-0294-7
DOI | PDF

Jin, L., Siegel, D.I., Lautz, L.K., and Otz, M.H., 2009,
Transient storage and downstream solute transport in nested stream reaches affected by beaver dams: Hydrological Processes, v. 23, no. 17, p. 2438-2449, doi:10.1002/hyp.7359
DOI | PDF

Johnson, Z.C., Warwick, J.J., and Schumer, R., 2014,
Factors affecting hyporheic and surface transient storage in a western U.S. river: Journal of Hydrology, v. 510, p. 325-339, doi: 10.1016/j.jhydrol.2013.12.037
DOI | PDF

Kaplan, L.A., Wiegner, T.N., Newbold, J.D., Ostrom, P.H., and Gandhi, H., 2008,
Untangling the complex issue of dissolved organic carbon uptake: A stable isotope approach: Freshwater Biology, v. 53, no. 5, p. 855-864, doi:10.1111/j.1365-2427.2007.01941.x
DOI | PDF

Kazezyilmaz-Alhan, C.M., and Medina Jr., M.A., 2006,
Stream solute transport incorporating hyporheic zone processes: Journal of Hydrology, v. 329, p. 26-38, doi:10.1016/j.jhydrol.2006.02.003
DOI | PDF

Keefe, S.H., Barber, L.B., Runkel, R.L., and Ryan, J.N., 2004,
Fate of volatile organic compounds in constructed wastewater treatment wetlands: Environmental Science & Technology, v. 38, no. 7, p. 2209-2216, doi:10.1021/es034661i
DOI | PDF

Keefe, S.H., Barber, L.B., Runkel, R.L., Ryan, J.N., McKnight, D.M., and Wass, R.D., 2004,
Conservative and reactive solute transport in constructed wetlands: Water Resources Research, v. 40, W01201, doi:10.1029/2003WR002130
DOI | PDF

Keefe, S. H., Daniels (Thullen), J.S., Runkel, R.L., Wass, R.D., Stiles, E.A., and Barber, L.B., 2010,
Influence of hummocks and emergent vegetation on hydraulic performance in a surface flow wastewater treatment wetland: Water Resources Research, v. 46, W11518, doi:10.1029/2010WR009512
DOI | PDF

Kelleher, C., Wagener, T., McGlynn, B., Ward, A. S., Gooseff, M. N., and Payn, R. A., 2013,
Identifiability of transient storage model parameters along a mountain stream: Water Resources Research, v. 49, no. 9, p. 5290-5306, doi: 10.1002/wrcr.20413
DOI | PDF

Knust, A.E., and Warwick, J.J., 2009,
Using a fluctuating tracer to estimate hyporheic exchange in restored and unrestored reaches of the Truckee River, Nevada, USA: Hydrological Processes, v. 23, no. 8, p. 1119-1130, doi:10.1002/hyp.7218
DOI | PDF

Koch, J.C., Runkel, R.L., Striegl, R., and McKnight, D.M., 2013,
Hydrologic controls on the transport and cycling of carbon and nitrogen in a boreal catchment underlain by continuous permafrost: Journal of Geophysical Research: Biogeosciences, v. 118, no.2, p. 698-712, doi: 10.1002/jgrg.20058
DOI | PDF

Kupilas, B., Hering, D., Lorenz, A.W., Knuth, C., and Gücker, B., 2017,
Hydromorphological restoration stimulates river ecosystem metabolism: Biogeosciences, v. 14, p. 1989-2002, doi: 10.5194/bg-14-1989-2017
DOI | PDF

Laeanen A., and Bencala, K.E., 2001,
Transient storage assessment of dye-tracer injections in rivers of the Willamette Basin, Oregon: Journal of the American Water Resources Association, v. 37, no. 2, p. 367-377, doi:10.1111/j.1752-1688.2001.tb00975.x
DOI | PDF

Lamontagne, S., and Cook, P.G., 2007,
Estimation of hyporheic water residence time in situ using 222Rn disequilibrium: Limnology and Oceanography: Methods, v. 5, p. 407-416
DOI | PDF

Lautz, L.K., Siegel, D.I., and Bauer, R.L., 2006,
Impact of debris dams on hyporheic interaction along a semi-arid stream: Hydrological Processes, v. 20, no. 1, p. 183-196, doi:10.1002/hyp.5910
DOI | PDF

Lautz, L.K., and Siegel, D.I., 2007,
The effect of transient storage on nitrate uptake lengths in streams: an inter-site comparison: Hydrological Processes, v. 21, no. 26, p. 3533-3548, doi:10.1002/hyp.6569
DOI | PDF

Lees, M.J., Camacho, L.A., and Chapra, S.C., 2000,
On the relationship of transient-storage and aggregated dead zone models to solute transport in streams: Water Resources Research, v. 36, no. 1, p. 213-224. doi:10.1029/1999WR900265
DOI | PDF

Lottig, N.R., Valett, H.M., Schreiber, M.E., and Webster, J.R., 2007,
Flooding and arsenic contamination: Influences on ecosystem structure and function in an Appalachian headwater stream: Limnology and Oceanography, v. 52, no. 5, p. 1991-2001, doi:10.4319/lo.2007.52.5.1991
DOI | PDF

Magirl, C.S., et al., 2011,
Baseline hydrologic studies in the lower Elwha prior to dam removal: In: Coastal Habitats of the Elwha River, Washington - Biological and Physical Patterns and Processes prior to Dam removal, U.S. Geological Survey Scientific Investigation Report 2011-5120, eds. Duda, J.J., Warrick, J.A., and Magirl, C.S.
HTML

Malcolm, I.A., Middlemas, C.A., Soulsby, C., Middlemas, S.J., and Youngson, A.F., 2010,
Hyporheic zone processes in a canalised agricultural stream: implications for salmonid embryo survival: Fundamental and Applied Limnology / Archiv für Hydrobiologie, v. 176, no. 4, p. 319-336, doi:10.1127/1863-9135/2010/0176-0319
DOI

Masud Rana, S.M., Scott, D.T., and Hester, E.T., 2017,
Effects of in-stream structures and channel flow rate variation on transient storage: Journal of Hydrology, v. 548, p. 157-169, doi: 10.1016/j.jhydrol.2017.02.049
DOI | PDF

Martinez, C.J., and Wise, W.R., 2003,
Analysis of constructed treatment wetland hydraulics with the transient storage model OTIS: Ecological Engineering, v. 20, p. 211-222, doi:10.1016/S0925-8574(03)00029-6
DOI | PDF

McKnight, D.M., Kimball, B.A., and Runkel, R.L., 2001,
pH dependence of iron photoreduction in a Rocky Mountain stream affected by acid mine drainage: Hydrological Processes, v. 15, p. 1979-1992, doi:10.1002/hyp.251
DOI | PDF

McKnight, D.M., Hornberger, G.M., Bencala, K.E., and Boyer, E.W., 2002,
In-stream sorption of fulvic acid in an acidic stream: A stream-scale transport experiment: Water Resources Research, v. 38, no. 1, doi:10.1029/2001WR000269
DOI | PDF

McKnight, D.M., Runkel, R.L., Tate, C.M., Duff, J.H., Moorhead, D.L., 2004,
Inorganic N and P dynamics of Antarctic glacial meltwater streams as controlled by hyporheic exchange and benthic autotrophic communities: Journal of the North American Benthological Society, v. 23, no. 2, p. 171-188.
DOI | PDF

Menichino, G.T., Scott, D.T., and Hester, E.T., 2015,
Abundance and dimensions of naturally occurring macropores along stream channels and the effects of artificially constructed large macropores on transient storage: Freshwater Science, v. 34, no. 1, p. 125-138, doi: 10.1086/679655
DOI | PDF

Miller, M.P., McKnight, D.M., Cory, R.M., Williams, M.W., and Runkel, R.L., 2006,
Hyporheic exchange and fulvic acid redox reactions in an alpine stream/wetland ecosystem, Colorado front range: Environmental Science and Technology, v. 40, no. 19, p. 5943-5949, doi:10.1021/es060635j
DOI | PDF

Morrice, J.A., Valett, H.M., Dahm, C.N., and Campana, M.E., 1997,
Alluvial characteristics, groundwater-surface water exchange and hydrological retention in headwater streams: Hydrological Processes, v. 11, p. 253-267, doi:10.1002/(SICI)1099-1085(19970315)11:3<253::AID-HYP439>3.0.CO;2-J
DOI | PDF

Mueller Price, J., Bledsoe, B.P., and Baker, D.W., 2015,
Influences of sudden changes in discharge and physical stream characteristics on transient storage and nitrate uptake in an urban stream: Hydrological Processes, v. 29, p. 1466-1479, doi: 10.1002/hyp.10275
DOI | PDF

Mueller Price, J.S., Baker, D.W., and Bledsoe, B.P., 2016,
Effects of passive and structural stream restoration approaches on transient storage and nitrate uptake: River Research Applications, v. 32, no. 7, p. 1542-1554, doi: 10.1002/rra.3013
DOI | PDF

Mukherjee, A, Fryar, A.E., and Lasage, D.M., 2005,
Using tracer tests to assess natural attenuation of contaminants along a channelized coastal plain stream: Environmental & Engineering Geoscience, v. XI, no. 4, p. 371-382, doi:10.2113/11.4.371
DOI | PDF

Mulholland P.J., et al., 2008,
Stream denitrification across biomes and its response to anthropogenic nitrate loading: Nature, v. 452, p. 202-205, doi:10.1038/nature06686
DOI | PDF

Mulholland, P.J., Hall, R.O. Jr., Sobota, D.J., Dodds, W.K., Findlay, S.E.G., Grimm, N.B., Hamilton, S.K., McDowell, W.H., et al., 2009,
Nitrate removal in stream ecosystems measured by 15N addition experiments: Denitrification: Limnology and Oceanography, v. 54, no. 3, p. 666-680
DOI | PDF

Neill, C., Deegan, L.A., Thomas, S.M., Haupert, C.L., Krusche, A.V., Ballester, V.M., and Victoria, R.L., 2006,
Deforestation alters the hydraulic and biogeochemical characteristics of small lowland Amazonian streams: Hydrological Processes, v. 20, no. 12, p. 2563-2580, doi:10.1002/hyp.6216
DOI | PDF

Olson, J.C., Marcarelli, A.M., Timm, A.L., Eggert, S.L., and Kolka, R.K., 2017,
Evaluating the effects of culvert designs on ecosystem processes in northern Wisconsin streams: River Research and Applications, v. 33, p. 777-787, doi: 10.1002/rra.3121
DOI | PDF

Orr, C.H., Rogers, K.L., and Stanley, E.H., 2006,
Channel morphology and P uptake following removal of a small dam: Journal of the North American Benthological Society, v. 25, no.3, p. 556-568, doi:10.1899/0887-3593(2006)25[556:CMAPUF]2.0.CO;2
DOI | PDF

Orr, C.H., Clark, J.J., Wilcock, P.R., Finlay, J.C., Doyle, M.W., 2009,
Comparison of morphological and biological control of exchange with transient storage zones in a field-scale flume: Journal of Geophysical Research, v. 114, G02019, doi:10.1029/2008JG000825
DOI | PDF

Phanikumar, M.S., Aslam, I., Shen, C., Long, D.T., and Voice, T.C., 2007,
Separating surface storage from hyporheic retention in natural streams using wavelet decomposition of acoustic Doppler current profiles: Water Resources Research, v. 43, W05406, doi:10.1029/2006WR005104
DOI | PDF

Potter, J.D., McDowell, W.H., Merriam, J.L., Peterson, B.J., and Thomas, S.M., 2010,
Denitrification and total nitrate uptake in streams of a tropical landscape: Ecological Applications, v. 20, no. 8, p. 2104-2115, doi: 10.1890/09-1110.1
DOI | PDF

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

Powers, S., Johnson, R., Stanley, E., 2012,
Nutrient retention and the problem of hydrologic disconnection in streams and wetlands: Ecosystems, v. 15, no. 3, p. 435-449 doi: 10.1007/s10021-012-9520-8
DOI | PDF

Rivord, J., Saito, L., Miller, G., and Stoddard, S., 2014,
Modeling contaminant spills in the Truckee River in the western United States: Journal of Water Resource Planning and Management, v. 140, no. 3, p. 343–354, doi: 10.1061/%28ASCE%29WR.1943-5452.0000338
DOI | PDF

Ruehl, C., Fisher, A.T., Hatch, C., Los Huertos, M., Stemler, G., and Shennan, C., 2006,
Differential gauging and tracer tests resolve seepage fluxes in a strongly-losing stream: Journal of Hydrology, v. 330, p. 235-248, doi:10.1016/j.jhydrol.2006.03.025
DOI | PDF

Ruehl, C.R., Fisher, A.T., Los Huertos, M., Wankel, S.D., Wheat, C.G., Kendall, C., Hatch, C.E., and Shennan, C., 2007,
Nitrate dynamics within the Pajaro River, a nutrient-rich, losing stream: Journal of the North American Benthological Society, v. 26, no. 2, p. 191-206, doi:10.1899/0887-3593(2007)26[191:NDWTPR]2.0.CO;2
DOI | PDF

Runkel, R.L., McKnight, D.M., and Andrews E.D., 1998,
Analysis of transient storage subject to unsteady flow: Diel flow variation in an Antarctic stream: Journal of North American Benthological Society, v. 17, no. 2, p 143-154.
URL | PDF

Runkel, R. L., 2015,
On the use of rhodamine WT for the characterization of stream hydrodynamics and transient storage: Water Resources Research, v. 51, p. 6125-6142, doi:10.1002/2015WR017201
DOI | PDF

Ryan, R.J., Packman, A.I., and Welty, C., 2004,
Estimation of solute transport and storage parameters in a stream with anthropogenically produced unsteady flow and industrial bromide input: Water Resources Research, v. 40, no. 1, p. W016021-W016026, doi:10.1029/2003WR002458
DOI | PDF

Ryan, R.J., and Packman, A.I., 2006,
Changes in streambed sediment characteristics and solute transport in the headwaters of Valley Creek, an urbanizing watershed: Journal of Hydrology, v. 323, p. 74-91, doi:10.1016/j.jhydrol.2005.06.042
DOI | PDF

Ryan, R.J., Welty, C., Larson, P.C, 2010,
Variation in surface water-groundwater exchange with land use in an urban stream: Journal of Hydrology v. 392, p. 1-11, doi:10.1016/j.jhydrol.2010.06.004
DOI | PDF

Salehin, M., Packman, A.I., and Wörman, A., 2003,
Comparison of transient storage in vegetated and unvegetated reaches of a small agricultural stream in Sweden: Seasonal variation and anthropogenic manipulation: Advances in Water Resources, v. 26, no. 9, p. 951-964, doi:10.1016/S0309-1708(03)00084-8
DOI | PDF

Scanlon, T.M., Ingram, S.M., and Riscassi, A.L., 2010,
Terrestrial and in-stream influences on the spatial variability of nitrate in a forested headwater catchment: Journal of Geophysical Research, v. 115, G02022, doi:10.1029/2009JG001091
DOI | PDF

Schmid, B., 2008,
Can longitudinal solute transport parameters be transferred to different flow rates?: Journal of Hydrologic Engineering, v. 13, no. 6, p. 505-509, doi:10.1061/(ASCE)1084-0699(2008)13:6(505)
DOI | PDF

Schmid, B.H., Innocenti, I., Sanfilippo, U., 2010,
Characterizing solute transport with transient storage across a range of flow rates: The evidence of repeated tracer experiments in Austrian and Italian streams: Advances in Water Resources, v. 33, no. 11, p. 1340-1346, doi: 10.1016/j.advwatres.2010.06.001
DOI | PDF

Schuetz, T., Weiler, M., and Lange, J., 2012,
Multitracer assessment of wetland succession: Effects on conservative and nonconservative transport processes: Water Resources Research, v. 48, W06538, doi:10.1029/2011WR011292
DOI | PDF

Schulz, M., Priegnitz, J., Klasmeier, J., Heller, S., Meinecke, S., and Feibicke, M., 2012,
Effect of bed surface roughness on longitudinal dispersion in artificial open channels: Hydrological Processes, v. 26, no. 2, p. 272-280, doi: 10.1002/hyp.8229
DOI | PDF

Scordo, E.B., and Moore, R.D., 2009,
Transient storage processes in a steep headwater stream: Hydrological Processes, v. 23, no. 18, p. 2671-2685, doi:10.1002/hyp.7345
DOI | PDF

Scott, D.T., McKnight, D.M., Voelker, B.M., and Hrncir, D.C., 2002,
Redox Processes Controlling Manganese Fate and Transport in a Mountain Stream: Environmental Science & Technology, v. 36, no. 3, p. 453-459, doi: 10.1021/es010951s
DOI | PDF

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.
DOI | PDF

Scott, D.T., Runkel, R.L., McKnight, D.M., Voelker, B.M., Kimball, B.A., and Carraway, E.R., 2003,
Transport and cycling of iron and hydrogen peroxide in a freshwater stream -- Influence of organic acids: Water Resources Research, v. 39, no. 11, 1308, doi:10.1029/2002WR001768
DOI | PDF

Scott, D., Hood, E., and Nassry, M., 2010,
In-stream uptake and retention of C, N and P in a supraglacial stream: Annals of Glaciology, v. 51, no. 56, p. 80–86, doi: 10.3189/172756411795932065
DOI

Sheibley, R.W., Duff, J.H., and Tesoriero, A.J., 2014,
Low transient storage and uptake efficiencies in seven agricultural streams: implications for nutrient demand: Journal of Environmental Quality, v. 43, no. 6, p. 1980-1990, doi: 10.2134/jeq2014.01.0034
DOI | PDF

Singha, K., Pidlisecky, A., Day-Lewis, F.D., and Gooseff, M.N., 2008,
Electrical characterization of non-Fickian transport in groundwater and hyporheic systems: Water Resources Research, v. 44, W00D07, doi:10.1029/2008WR007048
DOI | PDF

Sokác, M., 2017,
Determination of the longitudinal dispersion coefficient in lowland streams with occurrence of dead zones: “Environmental Engineering” 10th International Conference, Vilnius Gediminas Technical University, Lithuania, 27-28 April 2017
DOI | PDF

Stofleth, J.M., Shields, F.D., Fox, G.A., 2008,
Hyporheic and total transient storage in small, sand-bed streams: Hydrological Processes, v. 22, no. 12, p. 1885-1894, doi:10.1002/hyp.6773
DOI | PDF

Stolp, B.J., Solomon, D.K., Suckow, A., Vitvar, T., Rank, D., Aggarwal, P.K., and Han, L.F., 2010,
Age dating base flow at springs and gaining streams using helium-3 and tritium: Fischa-Dagnitz system, southern Vienna Basin, Austria: Water Resources Research, v. 46, W07503, doi:10.1029/2009WR008006
DOI | PDF

Story, A., Moore, R.D., and Macdonald, J.S., 2003,
Stream temperatures in two shaded reaches below cutblocks and logging roads: downstream cooling linked to subsurface hydrology: Canadian Journal of Forest Research, v. 33, p. 1383-1396, doi:10.1139/X03-087
DOI | PDF

Szeftel, P., Moore, R.D., Weiler, M., 2011,
Influence of distributed flow losses and gains on the estimation of transient storage parameters from stream tracer experiments: Journal of Hydrology, v. 396, p. 277-291 doi: 10.1016/j.jhydrol.2010.11.018
DOI | PDF

Tanio Y., Ohte, N., Fujimoto, M., and Sheibley, R.W., 2008,
Nitrate and phosphate uptake in a temperate forest stream in central Japan: In: From Headwaters to the Ocean: Hydrological Changes and Watershed Management, eds. Taniguchi, M., Burnett, W.C., Fukushima, Y., Haigh, M., Umezawa, Y., pp. 83-89, Taylor & Francis Group, London.
HTML

Tank, J.L., Rosi-Marshall, E.J., Baker, M.A., and Hall, R.O., 2008,
Are rivers just big streams? A pulse method to quantify nitrogen demand in a large river: Ecology, v. 89, no. 10, p. 2935-2945, doi:10.1890/07-1315.1
DOI | PDF

Tate, C.M., Broshears, R.E., and McKnight, D.M., 1995,
Phosphate dynamics in an acidic mountain stream: Interactions involving algal uptake, sorption by iron oxide, and photoreduction: Limnology and Oceanography, v. 40, no. 5, p. 938-946.
DOI | PDF

Tobias, C.R., Böhlke, J.K., Harvey, J.W., 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
DOI | PDF

Tromboni, F., Dodds, W.K., Neres-Lima, V., Zandona, E., and Moulton, T.P., 2017,
Heterogeneity and scaling of photosynthesis, respiration, and nitrogen uptake in three Atlantic Rainforest streams: Ecosphere, v. 8, no. 9, p. 1-19, doi: 10.1002/ecs2.1959
DOI | PDF

Turunen, J., Aroviita, J., Marttila, H., Louhi, P., Laamanen, T., Tolkkinen, M., Luhta, P.-L., Kløve, B. and Muotka, T., 2017,
Differential responses by stream and riparian biodiversity to in-stream restoration of forestry-impacted streams: Journal of Applied Ecology, v. 54, no. 5, p. 1505-1514, doi:10.1111/1365-2664.12897
DOI | PDF

Tych, W., and Young, P.C., 2012,
A Matlab software framework for dynamic model emulation: Environmental Modelling & Software, v. 34, p. 19-29, doi: 10.1016/j.envsoft.2011.08.008
DOI | PDF

Valett, H.M., Morrice, J.A., Dahm, C.N., and Campana, M.E., 1996,
Parent lithology, surface-groundwater exchange, and nitrate retention in headwater streams: Limnology and Oceanography, v. 41, no. 2, p. 333-345.
DOI | PDF

von Schiller, D., Martí, E., Riera, J.L., Ribot, M., Marks, J.C., and Sabater, F., 2008,
Influence of land use on stream ecosystem function in a Mediterranean catchment: Freshwater Biology, v. 53, no. 12, p. 2600-2612, doi:10.1111/j.1365-2427.2008.02059.x
DOI | PDF

von Schiller, D., Martí, E., and Riera, J.L., 2009,
Nitrate retention and removal in Mediterranean streams bordered by contrasting land uses: a 15N tracer study : Biogeosciences, v. 6, no. 2, p. 181-196, doi:10.5194/bg-6-181-2009
DOI | PDF

Walton-Day, K., Paschke, S.S., Runkel, R.L., and Kimball, B.A., 2007,
Using the OTIS solute-transport model to evaluate remediation scenarios in Cement Creek and the Upper Animas River (Chapter E24), in Church, S.E., von Guerard, P., and Finger, S.E., eds., Integrated Investigations of Environmental Effects of Historical Mining in the Animas River Watershed, San Juan County, Colorado: U.S. Geological Survey Professional Paper 1651, v. 2, p. 973-1028.
PDF

Walton-Day, K., Runkel, R.L., and Kimball, B.A., 2012,
Using spatially detailed water-quality data and solute-transport modeling to support Total Maximum Daily Load Development: Journal of the American Water Resources Association, v. 48, no. 5, p. 949-969, doi:10.1111/j.1752-1688.2012.00662.x
DOI | PDF

Wang, H., and Jawitz, J.W., 2006,
Hydraulic analysis of cell-network treatment wetlands: Journal of Hydrology, v. 330, p. 721-734, doi:10.1016/j.jhydrol.2006.05.005
DOI | PDF

Ward, A.S., Payn, R.A., Gooseff, M.N., McGlynn, B.L., Bencala, K.E., Kelleher, C.A., Wondzell, S.M., and Wagener, T., 2013,
Variations in surface water-ground water interactions along a headwater mountain stream: Comparisons between transient storage and water balance analyses: Water Resources Research, v. 49, no. 6, p. 3359-3374, doi: 10.1002/wrcr.20148
DOI | PDF

Ward, A.S., Kelleher, C.A., Mason, S.J.K., Wagener, T., McIntyre, N., McGlynn, B., Runkel, R.L., and Payn, R.A., 2017,
A software tool to assess uncertainty in transient-storage model parameters using Monte Carlo simulations: Freshwater Science, v. 36, no. 1, p. 195-217, doi: 10.1086/690444
DOI | PDF

Weigelhofer, G., Fuchsberger, J., Teufl, B., Welti, N., and Hein, T., 2012,
Effects of riparian forest buffers on in-stream nutrient retention in agricultural catchments: Journal of Environmental Quality, v. 41, no. 2, p. 373-379. doi: 10.2134/jeq2010.0436
DOI | PDF

Weigelhofer, G., Welti, N., Hein, T., 2013,
Limitations of stream restoration for nitrogen retention in agricultural headwater streams : Ecological Engineering, v. 60, p. 224-234, doi: 10.1016/j.ecoleng.2013.07.057
DOI | PDF

Weigelhofer, G., 2016,
The potential of agricultural headwater streams to retain soluble reactive phosphorus: Hydrobiologia, v. 793, no. 1, p. 149-160, doi: 10.1007/s10750-016-2789-4
DOI | PDF

Wondzell, S.M., 2006,
Effect of morphology and discharge on hyporheic exchange flows in two small streams in the Cascade Mountains of Oregon, USA: Hydrological Processes, v. 20, no. 2, p. 267-287, doi:10.1002/hyp.5902
DOI | PDF

Writer, J.H., Ryan, J.N., Keefe, S.H., Barber, L.B., 2011
Fate of 4-Nonylphenol and 17Β-Estradiol in the Redwood River of Minnesota: Environmental Science & Technology, v. 46, no. 2, p. 860-868, doi: 10.1021/es2031664
DOI | PDF

Zhou, Y., Wilson, G.V., Fox, G.A., Rigby, J.R., and Dabney, S.M., 2016,
Soil pipe flow tracer experiments: 2. Application of a streamflow transient storage zone model: Hydrological Processes, v. 30, no. 8, p. 1280-1291, doi: 10.1002/hyp.10712
DOI | PDF

USGS Home Water Climate Change Core Science Ecosystems Energy and Minerals Env. Health Hazards

Accessibility FOIA Privacy Policies and Notices

USA.gov logo U.S. Department of the Interior | U.S. Geological Survey
URL: https://water.usgs.gov/software/OTIS/apps/index.html
Page Contact Information: Rob Runkel
Page Last Modified: Wednesday, 10-Jan-2018 17:32:01 EST