Articles | Volume 29, issue 20
https://doi.org/10.5194/hess-29-5383-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/hess-29-5383-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
21 Oct 2025
Research article |
| 21 Oct 2025
| 21 Oct 2025
Explicit simulation of microbial transport with a dual-permeability, two-site kinetic deposition formulation using the integrated surface–subsurface hydrological model HydroGeoSphere
Friederike Currle
CORRESPONDING AUTHOR
Hydrogeology, Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland
René Therrien
Department of Geology and Geological Engineering, Université Laval, Québec, QC, Canada
Oliver S. Schilling
Hydrogeology, Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland
Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, 8600, Switzerland
Related authors
Friederike Currle, René Therrien, and Oliver S. Schilling
EGUsphere, https://doi.org/10.5194/egusphere-2024-3787, https://doi.org/10.5194/egusphere-2024-3787, 2024
Preprint withdrawn
Short summary
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We present a new approach to simulate the transport of microbes in river-aquifer systems in the integrated hydrological model HydroGeoSphere. Compared to existing models, the advantage of the new implementation lies in the consideration of all relevant parts of the water budget and the flexibility to simulate in parallel the reactive transport of several microbial species and solutes. The new developed tool enables to improve our understanding of pathogen transport in river-groundwater systems.
Love Råman Vinnå, Vidushi Bigler, Oliver S. Schilling, and Jannis Epting
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River water temperature is a key factor for water quality. Under climate change, inland water temperatures have increased, putting pressure on aquatic life and reducing the potential for human use. Here, future river water temperatures for Switzerland are studied. Results show that to the end of the 21st century, average river water temperatures will likely increase by 3.1±0.7 °C. This is likely to increases the thermal stress on sensitive aquatic species such as the brown trout.
Friederike Currle, René Therrien, and Oliver S. Schilling
EGUsphere, https://doi.org/10.5194/egusphere-2024-3787, https://doi.org/10.5194/egusphere-2024-3787, 2024
Preprint withdrawn
Short summary
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We present a new approach to simulate the transport of microbes in river-aquifer systems in the integrated hydrological model HydroGeoSphere. Compared to existing models, the advantage of the new implementation lies in the consideration of all relevant parts of the water budget and the flexibility to simulate in parallel the reactive transport of several microbial species and solutes. The new developed tool enables to improve our understanding of pathogen transport in river-groundwater systems.
Qi Tang, Hugo Delottier, Wolfgang Kurtz, Lars Nerger, Oliver S. Schilling, and Philip Brunner
Geosci. Model Dev., 17, 3559–3578, https://doi.org/10.5194/gmd-17-3559-2024, https://doi.org/10.5194/gmd-17-3559-2024, 2024
Short summary
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We have developed a new data assimilation framework by coupling an integrated hydrological model HydroGeoSphere with the data assimilation software PDAF. Compared to existing hydrological data assimilation systems, the advantage of our newly developed framework lies in its consideration of the physically based model; its large selection of different assimilation algorithms; and its modularity with respect to the combination of different types of observations, states and parameters.
Cited articles
Abdul, A. S.: Experimental and numerical studies of the effect of the capillary fringe on streamflow generation, PhD thesis, University of Waterloo, Waterloo, Ontario, Canada, 1985.
Aeschbach-Hertig, W. and Solomon, D. K.: Noble Gas Thermometry in Groundwater Hydrology, in: The Noble Gases as Geochemical Tracers, edited by: Burnard, P., Springer Berlin Heidelberg, Berlin, Heidelberg, https://doi.org/10.1007/978-3-642-28836-4_5, 81–122, 2013.
Aquanty Inc.: HydroGeoSphere Theory Manual, HGS version 2674, Aquanty Inc., Waterloo, Ontario, Canada, 2024.
Beisman, J. J., Maxwell, R. M., Navarre-Sitchler, A. K., Steefel, C. I., and Molins, S.: ParCrunchFlow: an efficient, parallel reactive transport simulation tool for physically and chemically heterogeneous saturated subsurface environments, Computational Geosciences, 19, 403–422, https://doi.org/10.1007/s10596-015-9475-x, 2015.
Besmer, M. D., Epting, J., Page, R. M., Sigrist, J. A., Huggenberger, P., and Hammes, F.: Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment, Scientific Reports, 6, 38462, https://doi.org/10.1038/srep38462, 2016.
Beyerle, U., Aeschbach-Hertig, W., Hofer, M., Imboden, D. M., Baur, H., and Kipfer, R.: Infiltration of river water to a shallow aquifer investigated with
Bixio, A., Gambolati, G., Paniconi, C., Putti, M., Shestopalov, V., Bublias, V., Bohuslavsky, A., Kasteltseva, N., and Rudenko, Y.: Modeling groundwater-surface water interactions including effects of morphogenetic depressions in the Chernobyl exclusion zone, Environmental Geology, 42, 162–177, https://doi.org/10.1007/s00254-001-0486-7, 2002.
Blanc, T., Peel, M., Brennwald, M. S., Kipfer, R., and Brunner, P.: Efficient injection of gas tracers into rivers: A tool to study Surface water–Groundwater interactions, Water Res., 254, 121375, https://doi.org/10.1016/j.watres.2024.121375, 2024.
Blanford, W. J., Brusseau, M. L., Jim Yeh, T. C., Gerba, C. P., and Harvey, R.: Influence of water chemistry and travel distance on bacteriophage PRD-1 transport in a sandy aquifer, Water Res., 39, 2345–2357, https://doi.org/10.1016/j.watres.2005.04.009, 2005.
Bradford, S. A. and Harvey, R. W.: Future research needs involving pathogens in groundwater, Hydrogeology Journal, 25, 931, https://doi.org/10.1007/s10040-016-1501-0, 2017.
Bradford, S. A., Simunek, J., Bettahar, M., van Genuchten, M. T., and Yates, S. R.: Modeling Colloid Attachment, Straining, and Exclusion in Saturated Porous Media, Environ. Sci. Technol., 37, 2242–2250, https://doi.org/10.1021/es025899u, 2003.
Bradford, S. A., Torkzaban, S., Leij, F., Šimùnek, J., and van Genuchten, M. T.: Modeling the coupled effects of pore space geometry and velocity on colloid transport and retention, Water Resour. Res., 45, https://doi.org/10.1029/2008WR007096, 2009.
Bradford, S. A., Wang, Y., Kim, H., Torkzaban, S., and Šimùnek, J.: Modeling Microorganism Transport and Survival in the Subsurface, Journal of Environmental Quality, 43, 421–440, https://doi.org/10.2134/jeq2013.05.0212, 2014.
Bradford, S. A., Leij, F. J., Schijven, J., and Torkzaban, S.: Critical Role of Preferential Flow in Field-Scale Pathogen Transport and Retention, Vadose Zone Journal, 16, 1–13, https://doi.org/10.2136/vzj2016.12.0127, 2017.
Brand, P. and Wülser, R.: Online-Messung mikrobiolgischer Parameter – Überwachung von Fluss und Grundwasser mittels online-Analyseverfahren, Aqua & Gas, 6, 22–28, 2018.
Brennwald, M. S., Schmidt, M., Oser, J., and Kipfer, R.: A Portable and Autonomous Mass Spectrometric System for On-Site Environmental Gas Analysis, Environ. Sci. Technol., 50, 13455–13463, https://doi.org/10.1021/acs.est.6b03669, 2016.
Brooks, L. E. and Field, K. G.: Bayesian meta-analysis to synthesize decay rate constant estimates for common fecal indicator bacteria, Water Res., 104, 262–271, https://doi.org/10.1016/j.watres.2016.08.005, 2016.
Brunner, P. and Simmons, C. T.: HydroGeoSphere: A Fully Integrated, Physically Based Hydrological Model, Groundwater, 50, https://doi.org/10.1111/j.1745-6584.2011.00882.x, 2012.
Brunner, P., Therrien, R., Renard, P., Simmons, C. T., and Franssen, H.-J. H.: Advances in understanding river-groundwater interactions, Rev. Geophys., 55, 818–854, https://doi.org/10.1002/2017RG000556, 2017.
Camporese, M., Paniconi, C., Putti, M., and Orlandini, S.: Surface-subsurface flow modeling with path-based runoff routing, boundary condition-based coupling, and assimilation of multisource observation data, Water Resour. Res., 46, https://doi.org/10.1029/2008WR007536, 2010.
Cecil, L. D. and Green, J. R.: Radon-222, in: Environmental Tracers in Subsurface Hydrology, edited by: Cook, P. G. and Herczeg, A. L., Springer, Boston, MA, https://doi.org/10.1007/978-1-4615-4557-6_6, 175–194, 2000.
Cook, P. and Herczeg, A.: Environmental Tracers in Subsurface Hydrology, Springer, 529 pp., https://doi.org/10.1007/978-1-4615-4557-6, 2000.
Currle, F., Therrien, R., and Schilling, O. S.: Supporting Information datasets for article: “Explicit simulation of reactive microbial transport with a dual-permeability, two-site kinetic deposition formulation using the integrated surface-subsurface hydrological model HydroGeoSphere”, HydroShare [data set], https://doi.org/10.4211/hs.84911fe3496f44eebbce512a6e8d0db3, 2025.
Dann, R., Close, M., Flintoft, M., Hector, R., Barlow, H., Thomas, S., and Francis, G.: Characterization and Estimation of Hydraulic Properties in an Alluvial Gravel Vadose Zone, Vadose Zone Journal, 8, 651–663, https://doi.org/10.2136/vzj2008.0174, 2009.
De Maet, T., Cornaton, F., and Hanert, E.: A scalable coupled surface–subsurface flow model, Computers & Fluids, 116, 74–87, https://doi.org/10.1016/j.compfluid.2015.03.028, 2015.
Delottier, H., Peel, M., Musy, S., Schilling, O. S., Purtschert, R., and Brunner, P.: Explicit simulation of environmental gas tracers with integrated surface and subsurface hydrological models, Frontiers in Water, 4, https://doi.org/10.3389/frwa.2022.980030, 2022.
Delottier, H., Doherty, J., and Brunner, P.: Data space inversion for efficient uncertainty quantification using an integrated surface and sub-surface hydrologic model, Geosci. Model Dev., 16, 4213–4231, https://doi.org/10.5194/gmd-16-4213-2023, 2023.
Delottier, H., Schilling, O. S., and Therrien, R.: Assessing the impact of surface water and groundwater interactions for regional-scale simulations of water table elevation, J. Hydrol., 639, 131641, https://doi.org/10.1016/j.jhydrol.2024.131641, 2024.
Derx, J., Blaschke, A. P., Farnleitner, A. H., Pang, L., Blöschl, G., and Schijven, J. F.: Effects of fluctuations in river water level on virus removal by bank filtration and aquifer passage — A scenario analysis, Journal of Contaminant Hydrology, 147, 34–44, https://doi.org/10.1016/j.jconhyd.2013.01.001, 2013.
Dong, H., Onstott, T. C., DeFlaun, M. F., Fuller, M. E., Scheibe, T. D., Streger, S. H., Rothmel, R. K., and Mailloux, B. J.: Relative Dominance of Physical versus Chemical Effects on the Transport of Adhesion-Deficient Bacteria in Intact Cores from South Oyster, Virginia, Environ. Sci. Technol., 36, 891–900, https://doi.org/10.1021/es010144t, 2002.
Ferguson, C., Husman, A. M. d. R., Altavilla, N., Deere, D., and Ashbolt, N.: Fate and Transport of Surface Water Pathogens in Watersheds, Critical Reviews in Environmental Science and Technology, 33, 299–361, https://doi.org/10.1080/10643380390814497, 2003.
Flynn, R. M., Hacini, Y., Schnegg, P.-A., Costa, R., and Diomande, K. A.: Use of Tracer Tests and Geophysical Logging to Understand Solute and Micro-organism Tracer Responses in Monitoring Wells with Long Screen Intervals in a Gravel Aquifer, Beitraege zur Hydrogeologie, 55, 5–20, 2006.
Gerke, H. H. and van Genuchten, M. T.: A dual-porosity model for simulating the preferential movement of water and solutes in structured porous media, Water Resour. Res., 29, 305–319, https://doi.org/10.1029/92WR02339, 1993.
Gutiérrez-Jurado, K. Y., Partington, D., Batelaan, O., Cook, P., and Shanafield, M.: What Triggers Streamflow for Intermittent Rivers and Ephemeral Streams in Low-Gradient Catchments in Mediterranean Climates, Water Resour. Res., 55, 9926–9946, https://doi.org/10.1029/2019WR025041, 2019.
Hoehn, E. and Von Gunten, H. R.: Radon in groundwater: A tool to assess infiltration from surface waters to aquifers, Water Resour. Res., 25, 1795–1803, https://doi.org/10.1029/WR025i008p01795, 1989.
Hollender, J., Rothardt, J., Radny, D., Loos, M., Epting, J., Huggenberger, P., Borer, P., and Singer, H.: Comprehensive micropollutant screening using LC-HRMS/MS at three riverbank filtration sites to assess natural attenuation and potential implications for human health, Water Research X, 1, 100007, https://doi.org/10.1016/j.wroa.2018.100007, 2018.
Hornstra, L. M., Schijven, J. F., Waade, A., Prat, G. S., Smits, F. J. C., Cirkel, G., Stuyfzand, P. J., and Medema, G. J.: Transport of bacteriophage MS2 and PRD1 in saturated dune sand under suboxic conditions, Water Res., 139, 158–167, https://doi.org/10.1016/j.watres.2018.03.054, 2018.
Hunt, R. J. and Johnson, W. P.: Pathogen transport in groundwater systems: contrasts with traditional solute transport, Hydrogeology Journal, 25, 921–930, https://doi.org/10.1007/s10040-016-1502-z, 2017.
HydroAlgorithmics Pty Ltd.: AlgoMesh2 User Guide [code], HydroAlgorithmics Pty Ltd, 2020.
Jones, J. P., Sudicky, E. A., Brookfield, A. E., and Park, Y. J.: An assessment of the tracer-based approach to quantifying groundwater contributions to streamflow, Water Resour. Res., 42, https://doi.org/10.1029/2005WR004130, 2006.
Kipfer, R., Aeschbach-Hertig, W., Peeters, F., and Stute, M.: Noble Gases in Lakes and Ground Waters, Reviews in Mineralogy and Geochemistry, 47, 615–700, https://doi.org/10.2138/rmg.2002.47.14, 2002.
Kirchner, J. W.: A double paradox in catchment hydrology and geochemistry, Hydrol. Process., 17, 871–874, https://doi.org/10.1002/hyp.5108, 2003.
Knabe, D., Guadagnini, A., Riva, M., and Engelhardt, I.: Uncertainty Analysis and Identification of Key Parameters Controlling Bacteria Transport Within a Riverbank Filtration Scenario, Water Resour. Res., 57, e2020WR027911, https://doi.org/10.1029/2020WR027911, 2021.
Kollet, S., Sulis, M., Maxwell, R. M., Paniconi, C., Putti, M., Bertoldi, G., Coon, E. T., Cordano, E., Endrizzi, S., Kikinzon, E., Mouche, E., Mügler, C., Park, Y.-J., Refsgaard, J. C., Stisen, S., and Sudicky, E.: The integrated hydrologic model intercomparison project, IH-MIP2: A second set of benchmark results to diagnose integrated hydrology and feedbacks, Water Resour. Res., 53, 867–890, https://doi.org/10.1002/2016WR019191, 2017.
Kötzsch, S. and Sinreich, M.: Zellzahlen zum Grundwasser: Bestimmung mittels Durchflusszytometrie: Wasserqualität, Aqua & Gas, 94, 14–21, 2014.
Kurtz, W., Lapin, A., Schilling, O. S., Tang, Q., Schiller, E., Braun, T., Hunkeler, D., Vereecken, H., Sudicky, E., Kropf, P., Hendricks Franssen, H.-J., and Brunner, P.: Integrating hydrological modelling, data assimilation and cloud computing for real-time management of water resources, Environ. Model. Software, 93, 418–435, https://doi.org/10.1016/j.envsoft.2017.03.011, 2017.
Kvitsand, H. M. L., Ilyas, A., and Østerhus, S. W.: Rapid bacteriophage MS2 transport in an oxic sandy aquifer in cold climate: Field experiments and modeling, Water Resour. Res., 51, 9725–9745, https://doi.org/10.1002/2015WR017863, 2015.
Leij, F. J. and Bradford, S. A.: Colloid transport in dual-permeability media, Journal of Contaminant Hydrology, 150, 65–76, https://doi.org/10.1016/j.jconhyd.2013.03.010, 2013.
Li, X., Scheibe, T. D., and Johnson, W. P.: Apparent Decreases in Colloid Deposition Rate Coefficients with Distance of Transport under Unfavorable Deposition Conditions: A General Phenomenon, Environ. Sci. Technol., 38, 5616–5625, https://doi.org/10.1021/es049154v, 2004.
Li, X., Zhang, P., Lin, C. L., and Johnson, W. P.: Role of Hydrodynamic Drag on Microsphere Deposition and Re-entrainment in Porous Media under Unfavorable Conditions, Environ. Sci. Technol., 39, 4012–4020, https://doi.org/10.1021/es048814t, 2005.
Loveland, J. P., Ryan, J. N., Amy, G. L., and Harvey, R. W.: The reversibility of virus attachment to mineral surfaces, Colloids Surf. Physicochem. Eng. Aspects, 107, 205–221, https://doi.org/10.1016/0927-7757(95)03373-4, 1996.
Mattle, N., Kinzelbach, W., Beyerle, U., Huggenberger, P., and Loosli, H. H.: Exploring an aquifer system by integrating hydraulic, hydrogeologic and environmental tracer data in a three-dimensional hydrodynamic transport model, J. Hydrol., 242, 183–196, https://doi.org/10.1016/S0022-1694(00)00394-2, 2001.
Maxwell, R. M., Putti, M., Meyerhoff, S., Delfs, J.-O., Ferguson, I. M., Ivanov, V., Kim, J., Kolditz, O., Kollet, S. J., Kumar, M., Lopez, S., Niu, J., Paniconi, C., Park, Y.-J., Phanikumar, M. S., Shen, C., Sudicky, E. A., and Sulis, M.: Surface-subsurface model intercomparison: A first set of benchmark results to diagnose integrated hydrology and feedbacks, Water Resour. Res., 50, 1531–1549, https://doi.org/10.1002/2013WR013725, 2014.
Maxwell, R. M., Kollet, S. J., Concon, L. E., Smith, S. G., Woodward, C. S., Falgout, R. D., Ferguson, I. M., Engdahl, N., Hokkanen, J., Artavanis, G., West, B., Yang, C., Hector, B., Gilbert, J., Bearup, L., Jefferson, J., Baldwin, C., Bosl, W. J., Hornung, R., Ashby, S., and Kulkarni, K. B.: ParFlow Documentation, International Ground Water Modeling Center Report GWMI, Integrated GroundWater Modeling Center, 2024.
Molnar, I. L., Johnson, W. P., Gerhard, J. I., Willson, C. S., and O'Carroll, D. M.: Predicting colloid transport through saturated porous media: A critical review, Water Resour. Res., 51, 6804–6845, https://doi.org/10.1002/2015WR017318, 2015.
Molson, J. W. and Frind, E. O.: On the use of mean groundwater age, life expectancy and capture probability for defining aquifer vulnerability and time-of-travel zones for source water protection, Journal of Contaminant Hydrology, 127, 76–87, https://doi.org/10.1016/j.jconhyd.2011.06.001, 2012.
Oudega, T. J., Lindner, G., Derx, J., Farnleitner, A. H., Sommer, R., Blaschke, A. P., and Stevenson, M. E.: Upscaling Transport of Bacillus subtilis Endospores and Coliphage phiX174 in Heterogeneous Porous Media from the Column to the Field Scale, Environ. Sci. Technol., 55, 11060–11069, https://doi.org/10.1021/acs.est.1c01892, 2021.
Paradis, D., Martel, R., Karanta, G., Lefebvre, R., Michaud, Y., Therrien, R., and Nastev, M.: Comparative Study of Methods for WHPA Delineation, Groundwater, 45, 158–167, https://doi.org/10.1111/j.1745-6584.2006.00271.x, 2007.
Partington, D., Brunner, P., Simmons, C. T., Therrien, R., Werner, A. D., Dandy, G. C., and Maier, H. R.: A hydraulic mixing-cell method to quantify the groundwater component of streamflow within spatially distributed fully integrated surface water–groundwater flow models, Environ. Model. Software, 26, 886–898, https://doi.org/10.1016/j.envsoft.2011.02.007, 2011.
Partington, D., Therrien, R., Simmons, C. T., and Brunner, P.: Blueprint for a coupled model of sedimentology, hydrology, and hydrogeology in streambeds, Rev. Geophys., 55, 287–309, https://doi.org/10.1002/2016RG000530, 2017.
Peel, M., Kipfer, R., Hunkeler, D., and Brunner, P.: Variable 222Rn emanation rates in an alluvial aquifer: Limits on using 222Rn as a tracer of surface water–groundwater interactions, Chemical Geology, 599, 120829, https://doi.org/10.1016/j.chemgeo.2022.120829, 2022.
Peel, M., Delottier, H., Kipfer, R., Hunkeler, D., and Brunner, P.: Exploring the reliability of 222Rn as a tracer of groundwater age in alluvial aquifers: Insights from the explicit simulation of variable 222Rn production, Water Res., 235, 119880, https://doi.org/10.1016/j.watres.2023.119880, 2023.
Popp, A. L., Pardo-Álvarez, Á., Schilling, O. S., Scheidegger, A., Musy, S., Peel, M., Brunner, P., Purtschert, R., Hunkeler, D., and Kipfer, R.: A Framework for Untangling Transient Groundwater Mixing and Travel Times, Water Resour. Res., 57, e2020WR028362, https://doi.org/10.1029/2020WR028362, 2021.
Ray, C.: Riverbank Filtration: Understanding Contaminant Biogeochemistry and Pathogen Removal, Springer, https://doi.org/10.1007/978-94-010-0479-4, 2002.
Ryan, J. N., Elimelech, M., Ard, R. A., Harvey, R. W., and Johnson, P. R.: Bacteriophage PRD1 and Silica Colloid Transport and Recovery in an Iron Oxide-Coated Sand Aquifer, Environ. Sci. Technol., 33, 63–73, https://doi.org/10.1021/es980350+, 1999.
Sasidharan, S.: Fate, transport and retention of viruses, bacteria and nanoparticles in saturated porous media, Thesis submitted for the degree of PhD, Flinders University of South Australia, Adelaide, Australia, 2016.
Sasidharan, S., Bradford, S. A., Šimùnek, J., and Torkzaban, S.: Minimizing Virus Transport in Porous Media by Optimizing Solid Phase Inactivation, Journal of Environmental Quality, 47, 1058–1067, https://doi.org/10.2134/jeq2018.01.0027, 2018.
Schijven, J. F. and Hassanizadeh, S. M.: Removal of Viruses by Soil Passage: Overview of Modeling, Processes, and Parameters, Critical Reviews in Environmental Science and Technology, 30, 49–127, https://doi.org/10.1080/10643380091184174, 2000.
Schijven, J. F. and Šimùnek, J.: Kinetic modeling of virus transport at the field scale, Journal of Contaminant Hydrology, 55, 113–135, https://doi.org/10.1016/S0169-7722(01)00188-7, 2002.
Schijven, J. F., Medema, G., Vogelaar, A. J., and Hassanizadeh, S. M.: Removal of microorganisms by deep well injection, Journal of Contaminant Hydrology, 44, 301–327, https://doi.org/10.1016/S0169-7722(00)00098-X, 2000.
Schilling, O. S., Gerber, C., Partington, D. J., Purtschert, R., Brennwald, M. S., Kipfer, R., Hunkeler, D., and Brunner, P.: Advancing Physically-Based Flow Simulations of Alluvial Systems Through Atmospheric Noble Gases and the Novel 37Ar Tracer Method, Water Resour. Res., 53, 10465–10490, https://doi.org/10.1002/2017WR020754, 2017.
Schilling, O. S., Cook, P. G., and Brunner, P.: Beyond Classical Observations in Hydrogeology: The Advantages of Including Exchange Flux, Temperature, Tracer Concentration, Residence Time, and Soil Moisture Observations in Groundwater Model Calibration, Rev. Geophys., 57, 146–182, https://doi.org/10.1029/2018RG000619, 2019.
Schilling, O. S., Cook, P. G., Grierson, P. F., Dogramaci, S., and Simmons, C. T.: Controls on Interactions Between Surface Water, Groundwater, and Riverine Vegetation Along Intermittent Rivers and Ephemeral Streams in Arid Regions, Water Resour. Res., 57, e2020WR028429, https://doi.org/10.1029/2020WR028429, 2021.
Schilling, O. S., Partington, D. J., Doherty, J., Kipfer, R., Hunkeler, D., and Brunner, P.: Buried Paleo-Channel Detection With a Groundwater Model, Tracer-Based Observations, and Spatially Varying, Preferred Anisotropy Pilot Point Calibration, Geophys. Res. Lett., 49, e2022GL098944, https://doi.org/10.1029/2022GL098944, 2022.
Šimùnek, J. and van Genuchten, M. T.: Modeling Nonequilibrium Flow and Transport Processes Using HYDRUS, Vadose Zone Journal, 7, 782–797, https://doi.org/10.2136/vzj2007.0074, 2008.
Šimùnek, J., Jacques, D., Langergraber, G., Bradford, S., Šejna, M., and Van Genuchten, M.: Numerical Modeling of Contaminant Transport Using HYDRUS and its Specialized Modules, Journal of the Indian Institute of Science, 92, 265–284, 2013.
Šimùnek, J., van Genuchten, M. T., and Šejna, M.: Recent Developments and Applications of the HYDRUS Computer Software Packages, Vadose Zone Journal, 15, vzj2016.2004.0033, https://doi.org/10.2136/vzj2016.04.0033, 2016.
Tang, Q., Kurtz, W., Schilling, O. S., Brunner, P., Vereecken, H., and Hendricks Franssen, H. J.: The influence of riverbed heterogeneity patterns on river-aquifer exchange fluxes under different connection regimes, J. Hydrol., 554, 383–396, https://doi.org/10.1016/j.jhydrol.2017.09.031, 2017.
Tang, Q., Delottier, H., Kurtz, W., Nerger, L., Schilling, O. S., and Brunner, P.: HGS-PDAF (version 1.0): a modular data assimilation framework for an integrated surface and subsurface hydrological model, Geosci. Model Dev., 17, 3559–3578, https://doi.org/10.5194/gmd-17-3559-2024, 2024.
Therrien, R. and Sudicky, E. A.: Three-dimensional analysis of variably-saturated flow and solute transport in discretely-fractured porous media, Journal of Contaminant Hydrology, 23, 1–44, https://doi.org/10.1016/0169-7722(95)00088-7, 1996.
Thomas, N. W., Arenas, A. A., Schilling, K. E., and Weber, L. J.: Numerical investigation of the spatial scale and time dependency of tile drainage contribution to stream flow, J. Hydrol., 538, 651–666, https://doi.org/10.1016/j.jhydrol.2016.04.055, 2016.
Tufenkji, N.: Modeling microbial transport in porous media: Traditional approaches and recent developments, Adv. Water Resour., 30, 1455–1469, https://doi.org/10.1016/j.advwatres.2006.05.014, 2007.
Tufenkji, N. and Elimelech, M.: Deviation from the Classical Colloid Filtration Theory in the Presence of Repulsive DLVO Interactions, Langmuir, 20, 10818–10828, https://doi.org/10.1021/la0486638, 2004.
Tufenkji, N. and Elimelech, M.: Breakdown of Colloid Filtration Theory: Role of the Secondary Energy Minimum and Surface Charge Heterogeneities, Langmuir, 21, 841–852, https://doi.org/10.1021/la048102g, 2005.
Tufenkji, N., Ryan, J. N., and Elimelech, M.: The promise of bank filtration, Environ. Sci. Technol., 36, 422a–428a, https://doi.org/10.1021/es022441j, 2002.
Vogt, T., Hoehn, E., Schneider, P., Freund, A., Schirmer, M., and Cirpka, O. A.: Fluctuations of electrical conductivity as a natural tracer for bank filtration in a losing stream, Adv. Water Resour., 33, 1296–1308, https://doi.org/10.1016/j.advwatres.2010.02.007, 2010.
Wang, Y., Hammes, F., Boon, N., Chami, M., and Egli, T.: Isolation and characterization of low nucleic acid (LNA)-content bacteria, ISME J., 3, 889–902, https://doi.org/10.1038/ismej.2009.46, 2009.
Weill, S., Mouche, E., and Patin, J.: A generalized Richards equation for surface/subsurface flow modelling, J. Hydrol., 366, 9–20, https://doi.org/10.1016/j.jhydrol.2008.12.007, 2009.
Weiss, W. J., Bouwer, E. J., Aboytes, R., LeChevallier, M. W., O'Melia, C. R., Le, B. T., and Schwab, K. J.: Riverbank filtration for control of microorganisms: Results from field monitoring, Water Res., 39, 1990–2001, https://doi.org/10.1016/j.watres.2005.03.018, 2005.
Yao, K.-M., Habibian, M. T., and O'Melia, C. R.: Water and waste water filtration. Concepts and applications, Environ. Sci. Technol., 5, 1105–1112, 1971.
Zhang, P., Johnson, W. P., Scheibe, T. D., Choi, K. H., Dobbs, F. C., and Mailloux, B. J.: Extended tailing of bacteria following breakthrough at the Narrow Channel Focus Area, Oyster, Virginia, Water Resour. Res., 37, 2687–2698, https://doi.org/10.1029/2000WR000151, 2001.
Zhang, W., Li, S., Wang, S., Lei, L., Yu, X., and Ma, T.: Transport of Escherichia coli phage through saturated porous media considering managed aquifer recharge, Environmental Science and Pollution Research, 25, 6497–6513, https://doi.org/10.1007/s11356-017-0876-3, 2018.
Short summary
We present a new approach to simulate the transport of microbes in river–aquifer systems in the integrated hydrological model HydroGeoSphere. Compared to existing models, the advantage of the new implementation lies in the consideration of all relevant parts of the water budget and the flexibility to simulate in parallel the reactive transport of several microbial species and solutes. The new developed tool enables us to improve our understanding of pathogen transport in river–groundwater systems.
We present a new approach to simulate the transport of microbes in river–aquifer systems in the...
