Modeling Surface and Ground Water Hyporheic Zone Using MODFLOW, MT3D and RT3D Models

Document Type : Research Paper


1 M.Sc. Graduate of water resources engineering, Department of Water Engineering, College of Agricultural Sciences, University of Guilan, Rasht, Iran.

2 Assistant Professor, Department of Water Engineering, College of Agricultural Sciences, University of Guilan, Rasht, Iran.

3 Senior Hydrogeologist and Groundwater Modeller, Arcadis Canada, Toronto, Canada.


Hyporheic zone is an active area that groundwater and surface water are mixed together in that zone. Any existing contamination in the surface water can be transferred to groundwater through this zone. In this research, the hyporheic zone beneath Zarjoob River and above Foomanat Aquifer was investigated by modeling to understand the impact of river on groundwater quality. For this purpose, three stations and three nearby groundwater wells were selected and water samples were collected in Year 2006-2007. The hyporheic zone was modeled for TDS as conservative parameter and NO3 as non-conservative parameter. MODFLOW and MT3D were used to simulate TDS in the hyporheic zone in two seasons; the agricultural season and non-agricultural season. The results showed that the hyporheic zone in non-agricultural season is 20 m far from the river, while in the agricultural season it was significantly less than 20 m. The results also showed that the reduction rate of TDS in agricultural season was more than that in non-agricultural season. This could be due to more groundwater use and increase in groundwater flow velocity. In the next step, NO3 was simulated using MODFLOW and RT3D. The simulation was carried out for two scenarios; with and without biodegradation. The results showed that without considering biodegradation, the hyporheic zone would extend to 25 m far from the river while with biodegradation it would be reduced to 20 m.


Main Subjects

Ahlfeld, D. P. and Mulligan, A. E. (2000). Optimal management of flow in groundwater systems: an introduction to combining simulation models and optimization methods. Academic Press
Alizadeh, M. R., Nikoo, M. R., and Rakhshandehroo, G. R. (2017). Hydro-environmental management of groundwater resources: a fuzzy-based multi-objective compromise approach. Journal of Hydrology, 551, 540–554
Appelo, C. A. J. and Rolle, M. (2010). PHT3D: A reactive multicomponent transport model for saturated porous media. Ground Water, 48(5), 627–632
Bailey, R. T., Gates, T. K. and Ahmadi, M. (2014). Simulating reactive transport of selenium coupled with nitrogen in a regional-scale irrigated groundwater system. Journal of Hydrology, 515, 29–46
Bailey, R. T., Gates, T. K. and Romero, E. C. (2015). Assessing the effectiveness of land and water management practices on nonpoint source nitrate levels in an alluvial stream-aquifer system. Journal of Contaminant Hydrology, 179(3), 102–115.
Bailey, R. T., Morway, E. D., Niswonger, R. G. and Gates, T. K. (2013). Modeling variably saturated multispecies reactive groundwater solute transport with MODFLOW‐UZF and RT3D. Groundwater, 51(5), 752–761
Boano, F., Harvey, J. W., Marion, A., Packman, A. I., Revelli, R., Ridolfi, L. and Wörman, A. (2014). Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications. Reviews of Geophysics, 52(4), 603–679
Buss, S., Cai, Z., Cardenas, B., Fleckenstein, J., Hannah, D., Heppell, K. and Krause, S. (2009). The hyporheic handbook: a handbook on the groundwater-surfacewater interface and hyporheic zone for environmental managers. Environment Agency
Cardenas, M. B. (2015). Hyporheic zone hydrologic science: A historical account of its emergence and a prospectus. Water Resources Research, 51(5), 3601–3616
Cardenas, M. B., Wilson, J. L. and Zlotnik, V.A. (2004). Impact of heterogeneity, bed forms, and stream curvature on subchannel hyporheic exchange. Water Resources Research, 40, 1-13.
Clement, T. P., Sun, Y., Hooker, B. S. and Petersen, J. N. (1998). Modeling multispecies reactive transport in ground water. Groundwater Monitoring & Remediation, 18(2), 79–92
Costa, D., Burlando, P., Priadi, C. and Shie-Yui, L. (2016). The nitrogen cycle in highly urbanized tropical regions and the effect of river–aquifer interactions: The case of Jakarta and the Ciliwung River. Journal of Contaminant Hydrology, 192, 87–100
Costa, D., Burlando, P., Priadi, C. and Shie-Yui, L. (2016). The nitrogen cycle in highly urbanized tropical regions and the effect of river–aquifer interactions: The case of Jakarta and the Ciliwung River. Journal of contaminant hydrology, 192, 87–100
Ghodrati, A. R., Sobh Zahedi, S. and Dadashi, M. A. (2007). Investigation on Industrial Pollution of Zarjub River- Rasht City- Guilan Province. Journal of the Iranian Natural Resources, 60(1), 213-224.
Harbaugh, A.W. (2005). MODFLOW-2005, the U.S. Geological Survey Modular Ground-Water Model:The Ground-Water Flow Process, Techniques and Methods 6–A16. United States Geological Survey, Reston, Virginia, USA.
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, 34(4), 623–636
Hester, E. T., Hammond, B. and Scott, D. T. (2016). Effects of inset floodplains and hyporheic exchange induced by in-stream structures on nitrate removal in a headwater stream. Ecological Engineering, 97, 452–464.
Huang, J., Christ, J. A. and Goltz, M. N. (2008). An assembly model for simulation of large‐scale ground water flow and transport. Groundwater, 46(6), 882–892
Kasahara, T. and Wondzell, S. M. (2003). Geomorphic controls on hyporheic exchange flow in mountain streams. Water Resources Research, 39(1), SBH-3
Kim, H., Lee, K. and Lee, J. (2014). Numerical verification of hyporheic zone depth estimation using streambed temperature. Journal of Hydrology, 511, 861–869.
Kim, S. (2006). Numerical analysis of bacterial transport in saturated porous media. Hydrological Processes: An International Journal, 20(5), 1177–1186
Kim, S., Park, C., Kim, D. and Jury, W. A. (2003). Kinetics of benzene biodegradation by Pseudomonas aeruginosa: parameter estimation. Environmental Toxicology and Chemistry, 22(5), 1038–1045
Lautz, L. K., & Siegel, D. I. (2006). Modeling surface and ground water mixing in the hyporheic zone using MODFLOW and MT3D. Advances in Water Resources, 29(11), 1618–1633.
Mao, X., Prommer, H., Barry, D. A., Langevin, C. D., Panteleit, B. and Li, L. (2006). Three-dimensional model for multi-component reactive transport with variable density groundwater flow. Environmental Modelling & Software, 21(5), 615–628
Marie, P., Géraldine, P.-C., Dominique, T., Alexandre, B., Marina, A., Jérome, P. and Wolfram, K. (2014). Water quality evolution during managed aquifer recharge (MAR) in Indian crystalline basement aquifers: reactive transport modeling in the critical zone. Procedia Earth and Planetary Science, 10, 82–87
Martin, C., Molenat, J., Gascuel-Odoux, C., Vouillamoz, J.-M., Robain, H., Ruiz, L. and Aquilina, L. (2006). Modelling the effect of physical and chemical characteristics of shallow aquifers on water and nitrate transport in small agricultural catchments. Journal of Hydrology, 326(1–4), 25–42
Meghdadi, A. and Javar, N. (2018). Evaluation of nitrate sources and the percent contribution of bacterial denitri fi cation in hyporheic zone using isotope fractionation technique and multi-linear regression analysis. Journal of Environmental Management, 222(May), 54–65.
Mostaza-Colado, D., Carreño-Conde, F., Rasines-Ladero, R. and Iepure, S. (2018). Hydrogeochemical characterization of a shallow alluvial aquifer: 1 baseline for groundwater quality assessment and resource management. Science of The Total Environment, 639, 1110–1125
Ondeck, N. T., Bohl, D. D., Bovonratwet, P., McLynn, R. P., Cui, J. J., Shultz, B. N. and Grauer, J. N. (2018). Discriminative ability of commonly used indices to predict adverse outcomes after poster lumbar fusion: a comparison of demographics, ASA, the modified Charlson Comorbidity Index, and the modified Frailty Index. The Spine Journal, 18(1), 44–52.
Prommer, H., Barry, D. A. and Zheng, C. (2003). MODFLOW/MT3DMS‐based reactive multicomponent transport modeling. Groundwater, 41(2), 247–257.
Rahmawati, N., Vuillaume, J. F. and Purnama, I. L. S. (2013). Salt intrusion in Coastal and Lowland areas of Semarang City. Journal of Hydrology, 494, 146–159.
Reddy, K. R. and Patrick Jr, W. H. (1975). Effect of alternate aerobic and anaerobic conditions on redox potential, organic matter decomposition and nitrogen loss in a flooded soil. Soil Biology and Biochemistry, 7(2), 87–94.
Saba, N., Umar, R. and Ahmed, S. (2016). Assessment of groundwater quality of major industrial city of Central Ganga plain, Western Uttar Pradesh, India through mass transport modeling using chloride as contaminant. Groundwater for Sustainable Development, 2, 154–168.
Spanoudaki, K., Stamou, A. I. and Nanou-Giannarou, A. (2009). Development and verification of a 3-D integrated surface water-groundwater model. Journal of Hydrology, 375(3–4), 410–427.
Storey, R. G., Howard, K. W. F. and Williams, D. D. (2003). Factors controlling riffle‐scale hyporheic exchange flows and their seasonal changes in a gaining stream: A three‐dimensional groundwater flow model. Water Resources Research, 39(2), 1-8.
Tian, Y., Zheng, Y., Wu, B., Wu, X., Liu, J. and Zheng, C. (2015). Modeling surface water-groundwater interaction in arid and semi-arid regions with intensive agriculture. Environmental Modelling and Software, 63, 170–184.
Triana, E., Labadie, J. W., Gates, T. K. and Anderson, C. W. (2010). Neural network approach to stream-aquifer modeling for improved river basin management. Journal of Hydrology, 391(3–4), 235–247
Winter, T. C. (1998). Ground water and surface water: a single resource (Vol. 1139). DIANE Publishing Inc.
Woessner, W. W. (2017). Hyporheic Zones. Methods in Stream Ecology. Elsevier Inc.
Woessner, W.W. (2000). Stream and fluvial plain ground water interactions: rescaling hydrogeologic thought. Ground Water, 38(3), 423–429.
Zhang, J., Song, J., Long, Y., Kong, F., Wang, L., Zhang, Y. and Hui, Y. (2017). Seasonal variability of hyporheic water exchange of the Weihe River in Shaanxi Province, China. Ecological Indicators, 92, 278-287.
Zheng, C., Hill, M. C. and Hsieh, P. A. (2001). MODFLOW-2000, the US Geological Survey modular ground-water model: User guide to the LMT6 package, the linkage with MT3DMS for multi-species mass transport modeling.
Zheng, C., Hill, M. C., Cao, G. and Ma, R. (2012). MT3DMS: Model use, calibration, and validation. Transactions of the ASABE, 55(4), 1549–1559.