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The SWAT-CNP model integrates Century-based terrestrial C/N/P cycling with aquatic C/N/P dynamics based on QUAL2K/CE-QUAL-W2 frameworks. It is an extension of the previously published SWAT-Carbon model (available on the SWAT website).
Key features of the SWAT-CNP model include:
Simulation of POC/N/P, DOC/N/P, and DIC/N/P fluxes from terrestrial to aquatic ecosystems.
Sediment C/N/P fluxes modeled using the sediment diagenesis framework developed by Di Toro.
Capability to simulate greenhouse gases, including CO2, CH4, and N2O, from the water surface.
Simulation of both floating and bottom algae communities.
Flexibility to run simulations at hourly to daily time steps.
This comprehensive model provides a robust tool for studying carbon, nitrogen, and phosphorus dynamics across terrestrial and aquatic ecosystems.
Huang, Y., Qi, J., Mezbahuddin, S., Dyck, M., MacKenzie, D. and Faramarzi, M., 2026. Effects of soil moisture and winter hydrologic processes on soil phosphorous accumulation and loss in canola croplands of cold-region watersheds. Science of The Total Environment, 1010, p.181051.
Risal, A., Karki, R. and Qi, J., 2025. Integrating Remote Sensing with Watershed-Scale Ecohydrological Modeling in Diverse Forest and Agricultural Landscapes of the Upper Mississippi River Basin. Environmental Modelling & Software, p.106588.
Tijjani, S.B., Giri, S., Lathrop, R., Qi, J., Karki, R., Schäfer, K.V., Kaplan, M.B., Oleghe, E.E. and Dhakal, S., 2024. Modeling carbon dynamics from a heterogeneous watershed in the mid-Atlantic USA: A distributed-calibration and independent verification (DCIV) approach. Science of the Total Environment, 956, p.177271.
Wei, X., Hayes, D.J., Butman, D.E., Qi, J., Ricciuto, D.M. and Yang, X., 2024. Modeling exports of dissolved organic carbon from landscapes: a review of challenges and opportunities. Environmental Research Letters, 19(5), p.053001.
Liang, K., Qi, J., Zhang, X., Emmett, B., Johnson, J.M., Malone, R.W., Moglen, G.E. and Venterea, R.T., 2023. Simulated nitrous oxide emissions from multiple agroecosystems in the US Corn Belt using the modified SWAT-C model. Environmental Pollution, 337, p.122537.
Tijjani, S.B., Qi, J., Giri, S. and Lathrop, R., 2023. Modeling Land Use and Management Practices Impacts on Soil Organic Carbon Loss in an Agricultural Watershed in the Mid-Atlantic Region. Water, 15(20), p.3534.Du, X., Faramarzi, M., Qi, J., Lei, Q. and Liu, H., 2023. Investigating hydrological transport pathways of dissolved organic carbon in cold region watershed based on a watershed biogeochemical model. Environmental Pollution, 324, p.121390.
Liang, K., Qi, J., Zhang, X. and Deng, J., 2022. Replicating measured site-scale soil organic carbon dynamics in the US Corn Belt using the SWAT-C model. Environmental Modelling & Software, 158, p.105553.
Qi, J., Zhang, X., Yang, Q., Srinivasan, R., Arnold, J.G., Li, J., Waldholf, S.T. and Cole, J., 2020. SWAT ungauged: Water quality modeling in the Upper Mississippi River Basin. Journal of Hydrology, 584, p.124601.
Qi, J., Zhang, X., Lee, S., Wu, Y., Moglen, G.E. and McCarty, G.W., 2020. Modeling sediment diagenesis processes on riverbed to better quantify aquatic carbon fluxes and stocks in a small watershed of the Mid-Atlantic region. Carbon Balance and Management, 15(1), pp.1-14.
Qi, J., Du, X., Zhang, X., Lee, S., Wu, Y., Deng, J., Moglen, G.E., Sadeghi, A.M. and McCarty, G.W., 2020. Modeling riverine dissolved and particulate organic carbon fluxes from two small watersheds in the northeastern United States. Environmental Modelling & Software, 124, p.104601.
Du, X., Zhang, X., Mukundan, R., Hoang, L. and Owens, E.M., 2019. Integrating terrestrial and aquatic processes toward watershed scale modeling of dissolved organic carbon fluxes. Environmental Pollution, 249, pp.125-135.
Zhang, X., 2018. Simulating eroded soil organic carbon with the SWAT-C model. Environmental modelling & software, 102, pp.39-48.
Zhang, X., Izaurralde, R.C., Arnold, J.G., Williams, J.R. and Srinivasan, R., 2013. Modifying the soil and water assessment tool to simulate cropland carbon flux: model development and initial evaluation. Science of the Total Environment, 463, pp.810-822.
Soil water phase changes (Freeze-Thaw) based on the heater transfer theory.
Huang, Y., Qi, J., Mezbahuddin, S., Dyck, M., MacKenzie, D. and Faramarzi, M., 2026. Effects of soil moisture and winter hydrologic processes on soil phosphorous accumulation and loss in canola croplands of cold-region watersheds. Science of The Total Environment, 1010, p.181051.
Zhang, Y., Zhang, X., Ding, B., Qi, J., Marek, G.W., Feng, P., Li Liu, D., Srinivasan, R. and Chen, Y., 2025. Simulating vertical soil nitrate migration induced by freeze–thaw cycles. Journal of Hydrology, p.133451.
Xiong, L., Jiang, Y., Qi, J. and Huang, G., 2025. Improving regional soil water-salt management by modeling soil freezing-thawing processes in a cold-arid irrigation district, upper Yellow River basin. Journal of Hydrology: Regional Studies, 60, p.102544.
Zhang, X., Zhang, Y., Qi, J., Marek, G.W., Srinivasan, R., Feng, P., Hu, K., Liu, D.L. and Chen, Y., 2025. Effects of changes in freeze‐thaw cycles on soil hydrothermal dynamics and erosion degradation under global warming in the Black Soil Region. Water Resources Research, 61(3), p.e2024WR038318.
Li, B., Tan, L., Zhang, X., Qi, J., Marek, G.W., Feng, P., Liu, D.L., Luo, X., Srinivasan, R. and Chen, Y., 2024. Enhanced freeze‐thaw cycle altered the simulations of groundwater dynamics in a heavily irrigated basin in the temperate region of China. Water Resources Research, 60(9), p.e2023WR036151.
Qi, J., Li, S., Li, Q., Xing, Z., Bourque, C.P.A. and Meng, F.R., 2016. A new soil-temperature module for SWAT application in regions with seasonal snow cover. Journal of Hydrology, 538, pp.863-877.
Qi, J., Li, S., Li, Q., Xing, Z., Bourque, C.P.A. and Meng, F.R., 2016. Assessing an enhanced version of SWAT on water quantity and quality simulation in regions with seasonal snow cover. Water Resources Management, 30(14), pp.5021-5037.
Qi, J., Li, S., Yang, Q., Xing, Z. and Meng, F.R., 2017. SWAT setup with long-term detailed landuse and management records and modification for a micro-watershed influenced by freeze-thaw cycles. Water Resources Management, 31(12), pp.3953-3974.
Qi, J., Zhang, X. and Cosh, M.H., 2019. Modeling soil temperature in a temperate region: A comparison between empirical and physically based methods in SWAT. Ecological Engineering, 129, pp.134-143.
Qi, J., Zhang, X. and Wang, Q., 2019. Improving hydrological simulation in the Upper Mississippi River Basin through enhanced freeze-thaw cycle representation. Journal of Hydrology, 571, pp.605-618.
Wang, Q., Qi, J., Wu, H., Zeng, Y., Shui, W., Zeng, J. and Zhang, X., 2020. Freeze-Thaw cycle representation alters response of watershed hydrology to future climate change. Catena, 195, p.104767.
Wang, Q., Qi, J., Li, J., Cole, J., Waldhoff, S.T. and Zhang, X., 2020. Nitrate loading projection is sensitive to freeze-thaw cycle representation. Water Research, 186, p.116355.
Wang, Q., Qi, J., Qiu, H., Li, J., Cole, J., Waldhoff, S. and Zhang, X., 2021. Pronounced Increases in Future Soil Erosion and Sediment Deposition as Influenced by Freeze–Thaw Cycles in the Upper Mississippi River Basin. Environmental Science & Technology, 55(14), pp.9905-9915.
Qi, J., Lee, S., Du, X., Ficklin, D.L., Wang, Q., Myers, D., Singh, D., Moglen, G.E., McCarty, G.W., Zhou, Y. and Zhang, X., 2021. Coupling terrestrial and aquatic thermal processes for improving stream temperature modeling at the watershed scale. Journal of Hydrology, 603, p.126983.
SWAT-R https://github.com/junyuqi1984/SWAT-R.git
SWAT-R https://github.com/junyuqi1984/SWAT-R.git
Richards-equation-based soil water movement with the sub-daily time step.
Richards-equation-based soil water movement with the sub-daily time step.
Zhu, L., Wang, H. and Qi, J., 2024, July. Estimating Daily Root Zone Soil Moisture at 30 Meters Spatial Resolution by Assimilating Fused Surface Soil Moisture to a Modified Hydrological Model. In IGARSS 2024-2024 IEEE International Geoscience and Remote Sensing Symposium (pp. 5166-5170). IEEE.
Zhu, L., Qi, J., Wang, H., Zhou, M., Ye, Y., Li, Y., Tong, C., Deng, X., He, S. and Wang, K., 2023. Coupling SMAP Brightness Temperature Into SWAT Hydrological Model for 30-m Resolution Soil Moisture Retrievals. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 16, pp.8319-8333.
Qi, J., Zhang, X., McCarty, G.W., Sadeghi, A.M., Cosh, M.H., Zeng, X., Gao, F., Daughtry, C.S., Huang, C., Lang, M.W. and Arnold, J.G., 2018. Assessing the performance of a physically-based soil moisture module integrated within the Soil and Water Assessment Tool. Environmental Modelling & Software, 109, pp.329-341.
Qi, J., Zhang, X., Lee, S., Moglen, G.E., Sadeghi, A.M. and McCarty, G.W., 2019. A coupled surface water storage and subsurface water dynamics model in SWAT for characterizing hydroperiod of geographically isolated wetlands. Advances in Water Resources, 131, p.103380.
Qi, J., Lee, S., Zhang, X., Yang, Q., McCarty, G.W. and Moglen, G.E., 2020. Effects of surface runoff and infiltration partition methods on hydrological modeling: A comparison of four schemes in two watersheds in the Northeastern US. Journal of Hydrology, 581, p.124415.
Lee, S., Qi, J., Kim, H., McCarty, G.W., Moglen, G.E., Anderson, M., Zhang, X. and Du, L., 2021. Utility of Remotely Sensed Evapotranspiration Products to Assess an Improved Model Structure. Sustainability, 13(4), p.2375.
Luyao Zhu, Junyu Qi, Hongquan Wang, Mengmeng Zhou, Yang Ye, Yongjun Li, Cheng Tong, Xiaodong Deng, Shan He, Ke Wang. 2023. Coupling SMAP brightness temperature into SWAT hydrological model for 30-m resolution soil moisture retrievals. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing
The Physiological Processes Predicting Growth model integrated with SWAT to simulate forest biomass and biogeochemical processes
Karki, R., Qi, J., Zhang, X. and Srivastava, P., 2025. Evaluating SWAT-3PG simulation of hydrologic and water quality processes in a forested watershed: A case study in the St. Croix River Basin. Journal of Hydrology, 648, p.132393.
Karki, R., Qi, J., Gonzalez-Benecke, C.A., Zhang, X., Martin, T.A. and Arnold, J.G., 2023. SWAT-3PG: Improving forest growth simulation with a process-based forest model in SWAT. Environmental Modelling & Software, 164, p.105705.
Water, carbon, and nutrients cycling processes for Intermittent rivers (IR)
Llanos-Paez, O., Qi, J., Sabater, S. and Acuña, V., 2025. Simulating dissolved organic carbon dynamics in non-perennial rivers: a novel SWAT-IR modeling approach. Earth Systems and Environment, 9(3), pp.1715-1735.
Llanos-Paez, O., Qi, J., Gutierrez, N., Colls, M., Sabater, S. and Acuña, V., 2024. Dynamics of Organic Matter Transport, Storage, and Processing in a Non-perennial Mediterranean River Network. Ecosystems, 27(5), pp.636-654.
(Century/Daycent-based soil N cycling and N2O emission)
(Century/Daycent-based soil N cycling and N2O emission)
Muhammad Rizwan Shahid, Junyu Qi*, Bryan Emmett, Robert W Malone, Natalia Rogovska, Peter O’Brien, John Kovar, Anna Radke3, Gary Feyereisen, Kevin W. King, Mark Williams, Daniel Moriasi, Michael J Castellano. Modeling Nitrogen Fluxes in a Tile-Drained Cropping System in the Midwest Using an Enhanced SWAT Model. Agricultural Water Management (accepted)
Qi, J.*, Malone, R., Liang, K., Cole, K., Emmett, B., Moriasi, D., Shahid, M.R. and Castellano, M., 2025. Comparative modeling of nitrogen losses in a tile-drained watershed using SWAT model: uncertainty and calibration considerations. Frontiers in Environmental Science, 13, p.1651136.
Liang, K., Qi, J., Zhang, X., Emmett, B., Johnson, J.M., Malone, R.W., Moglen, G.E. and Venterea, R.T., 2023. Simulated nitrous oxide emissions from multiple agroecosystems in the US Corn Belt using the modified SWAT-C model. Environmental Pollution, 337, p.122537.
SWAT for coupled Water and Energy cycling from soil to stream
SWAT for coupled Water and Energy cycling from soil to stream
Aryal, Y., Ficklin, D.L., Myers, D.T., Qi, J., Knouft, J.H., Murchie, K.J. and Day, S., 2025. Climate-Driven Shifts in Stream Thermal Regimes of the Laurentian Great Lakes Basin: The Role of Rain-on-Snow Events. Authorea Preprints.
Qi, J., Lee, S., Du, X., Ficklin, D.L., Wang, Q., Myers, D., Singh, D., Moglen, G.E., McCarty, G.W., Zhou, Y. and Zhang, X., 2021. Coupling terrestrial and aquatic thermal processes for improving stream temperature modeling at the watershed scale. Journal of Hydrology, 603, p.126983.
Qi, J., Li, S., Li, Q., Xing, Z., Bourque, C.-A., Meng, F.-R., 2016. A new soil-temperature module for SWAT application in regions with seasonal snow cover. J. Hydrol. 538, 863–877.
Du, X., Shrestha, N.K., Ficklin, D.L., Wang, J., 2018. Incorporation of the equilibrium temperature approach in a Soil and Water Assessment Tool hydroclimatological stream temperature model. Hydrol. Earth Syst. Sci. 22 (4), 2343–2357.
Ficklin, D.L., Luo, Y., Stewart, I.T., Maurer, E.P., 2012. Development and application of a hydroclimatological stream temperature model within the Soil and Water Assessment Tool. Water Resour. Res. 48 (1) https://doi.org/10.1029/2011WR011256.
Dynamic CO2 concentration effects on stomatal conductance, LAI, and radiation use efficiency.
Dynamic CO2 concentration effects on stomatal conductance, LAI, and radiation use efficiency.
Wen, N., Qi, J., Wang, Y., Marek, G.W., Ale, S., Feng, P., Li Liu, D., Srinivasan, R. and Chen, Y., 2026. Effects of rising CO2 concentrations on water dynamics and yields for C3 and C4 crops under both irrigated and dryland conditions in the Texas High Plains. Environmental Modelling & Software, p.106859.
Wen, N., Wang, Y., Ding, B., Han, Y., Qi, J., Ale, S., Feng, P., Li Liu, D., Srinivasan, R. and Chen, Y., 2025. Assessing a dynamic CO2 input and response module in SWAT for simulating climate-induced phosphorus loss and economic costs. Journal of Hydrology, p.134200.
Wen, N., Marek, G.W., Srinivasan, R., Brauer, D.K., Qi, J., Wang, N., Han, Y., Zhang, X., Feng, P., Li Liu, D. and Chen, Y., 2024. Assessing the impacts of long-term climate change on hydrology and yields of diversified crops in the Texas High Plains. Agricultural Water Management, 302, p.108985.
Wen, N., Han, Y., Qi, J., Marek, G.W., Sun, D., Feng, P., Srinivasan, R., Li Liu, D. and Chen, Y., 2024. Improving hydrological modeling to close the gap between elevated CO2 concentration and crop response: Implications for water resources. Water research, 265, p.122279.
Zhang, Y., Han, Y., Wen, N., Qi, J., Zhang, X., Marek, G.W., Srinivasan, R., Feng, P., Liu, D.L., Hu, K. and Chen, Y., 2024. Assessing the response mechanisms of elevated CO2 concentration on various forms of nitrogen losses in the Golden Corn Belt. Water Resources Research, 60(7), p.e2024WR037226.
Li, B., Tan, L., Zhang, X., Qi, J., Marek, G.W., Li, Y., Dong, X., Zhao, W., Chen, T., Feng, P. and Liu, D.L., 2023. Modeling streamflow response under changing environment using a modified SWAT model with enhanced representation of CO 2 effects. Journal of Hydrology: Regional Studies, 50, p.101547.
Zhang, Y., Ge, J., Qi, J., Liu, H., Zhang, X., Marek, G.W., Yuan, C., Ding, B., Feng, P., Liu, D.L. and Srinivasan, R., 2023. Evaluating the effects of single and integrated extreme climate events on hydrology in the Liao River Basin, China using a modified SWAT-BSR model. Journal of Hydrology, 623, p.129772.
Zhang, Y., Liu, H., Qi, J., Feng, P., Zhang, X., Li Liu, D., Marek, G.W., Srinivasan, R. and Chen, Y., 2023. Assessing impacts of global climate change on water and food security in the black soil region of Northeast China using an improved SWAT-CO2 model. Science of the Total Environment, 857, p.159482.
Zhang, Y., Qi, J., Pan, D., Marek, G.W., Zhang, X., Feng, P., Liu, H., Li, B., Ding, B., Brauer, D.K. and Srinivasan, R., 2022. Development and testing of a dynamic CO2 input method in SWAT for simulating long-term climate change impacts across various climatic locations. Journal of Hydrology, 614, p.128544.
SWAT-TileP (Developing)
SWAT-TileP (Developing)
Phosphorus leaching via tile drainage and macropore flow, and the hydrologic connectivity between potholes and tile drainage systems.
Phosphorus leaching via tile drainage and macropore flow, and the hydrologic connectivity between potholes and tile drainage systems.
SWAT-LEACHM (Developing)
SWAT-LEACHM (Developing)
The Leaching Estimation And CHemistry Model integrated with SWAT to predict soil salinity and irrigation management effects
The Leaching Estimation And CHemistry Model integrated with SWAT to predict soil salinity and irrigation management effects
SWAT-DNDC (Developing)
SWAT-DNDC (Developing)
The DeNitrification-DeComposition model integrated with SWAT to simulate GHG emissions
CLMDSS (Climate, Landuse, and Management Decision Support System)
CLMDSS (Climate, Landuse, and Management Decision Support System)
Qi, J., Li, S., Bourque, C.P.A., Xing, Z. and Meng, F.R., 2018. Developing a decision support tool for assessing land use change and BMPs in ungauged watersheds based on decision rules provided by SWAT simulation. Hydrology and Earth System Sciences, 22(7), pp.3789-3806.
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