Guiding riparian management in a transboundary watershed through high resolution spatial statistical network models
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Spatially distributed prediction of streamflow and nitrogen export dynamics is essential for precision management of agricultural watersheds. While temporal deep learning models such as Long Short-Term Memory (LSTM) have shown strong performance at basin scales, their ability to generalize spatially is limited by insufficient representation of spatial dependencies and flow paths, particularly under data-scarce conditions. To address this gap, we propose HydroGraphNet, a knowledge-guided graph machine learning framework that integrates process-based knowledge and explicit spatial learning into temporal modeling. This framework incorporates directed graph topology to encode watershed connectivity and upstream inflows, with mass balance constraints to improve physical consistency. To enhance generalization in sparsely monitored regions, HydroGraphNet is pretrained on synthetic data generated by the SWAT+ (Soil and Water Assessment Tool Plus) model. We evaluated HydroGraphNet in the Upper Sangamon River Basin (44 HUC-12 subwatersheds, 2001–2020) against two LSTM baselines: a lumped basin-level model and a distributed variant. When benchmarked on SWAT+ simulations in pretraining, HydroGraphNet improved test NSEs by 8.9% (discharge) and 13.7% (NO₃–N load) in temporal extrapolation, and by 27.1% and 34.7% in spatial extrapolation, relative to the Lumped LSTM baseline. After fine-tuning with USGS monitoring data, the model achieved mean test NSE (KGE) scores of 0.768 (0.861) for discharge and 0.626 (0.664) for NO₃–N load, substantially outperforming baselines. Attribution analysis further highlighted the importance of upstream inflow representation and graph-based spatial learning in capturing cross-subwatershed dependencies. The model also reproduced seasonal hydrological and biogeochemical patterns consistent with known processes, demonstrating its robustness and process fidelity for spatially distributed prediction. Altogether, HydroGraphNet advances the integration of physical knowledge and spatially explicit learning in hydrological modeling, offering a generalizable framework for distributed modeling to support spatially targeted water quality management in data-scarce watersheds.
The second phase of the North America Multi-Model Ensemble (NMME-2) provides globally available Subseasonal-to-Seasonal (S2S) precipitation forecasts with a daily resolution. The S2S precipitation forecasts are getting increasing attention for their potentials in providing hydrometeorological forcing information for water resources planning at an extended range. However, the forecast skills of many existing S2S forecast products will significantly decrease when the lead time increases, hindering their applicability for watershed-scale hydrologic modeling. Therefore, forecast validation and large-scale evaluation are of great importance for water resources planning and hydrological applications. In this study, we comprehensively evaluate the S2S precipitation forecasts from the NMME-2 dataset over the contiguous United States (CONUS) and during the study period from 1982 to 2011. Three aspects of precipitation forecast capabilities are compared and analyzed: bias, skill scores, and the ability to predict extreme precipitation events. The Parameter-elevation Regressions on Independent Slopes Model (PRISM) is used as ground truth reference. Differs from other regional forecast validation study, we further examined and analyzed the dependences of NMME-2 precipitation forecast skills according to different seasonality, geographical locations, and lead times. Results show that the forecast biases are not sensitive to lead times but are seasonally dependent of all NMME-2 models. Overestimations are found in the Western U.S. in cooler seasons while underestimations are observed in the central regions of the U.S. in warmer seasons. The forecast skill of all individual NMME-2 models generally decreases as increases of lead times. The simple model averaging (SMA) of five NMME-2 models demonstrates a higher forecast skill than any individual NMME-2 models. Spatially, the highest forecast skill scores are observed at coastal areas in the Western U.S. with an one-week lead time. As compared to the historical resampled forecasts, NMME-2 also shows better performance in predicting extreme precipitation events above 99% percentiles and below 1% percentiles with higher probability of detections and lower false alarm ratios. Finally, the obtained results suggest the great potentials of NMME-2 precipitation forecasts in assisting ensemble hydrologic forecasts at the S2S scale over the CONUS.
A critical component of assessing the impacts of climate change on watershed ecosystems involves understanding the role that dissolved organic matter (DOM) plays in driving whole ecosystem metabolism. The hyporheic zone—a biogeochemical control point where ground water and river water mix—is characterized by high DOM turnover and microbial activity and is responsible for a large fraction of lotic respiration. Yet, the dynamic nature of this ecotone provides a challenging but important environment to parse out different DOM influences on watershed function and net carbon and nutrient fluxes. We used high-resolution Fourier-transform ion cyclotron resonance mass spectrometry to provide a detailed molecular characterization of DOM and its transformation pathways in the Columbia river watershed. Samples were collected from ground water (adjacent unconfined aquifer underlying the Hanford 300 Area), Columbia river water, and its hyporheic zone. The hyporheic zone was sampled at five locations to capture spatial heterogeneity within the hyporheic zone. Our results revealed that abiotic transformation pathways (e.g., carboxylation), potentially driven by abiotic factors such as sunlight, in both the ground water and river water are likely influencing DOM availability to the hyporheic zone, which could then be coupled with biotic processes for enhanced microbial activity. The ground water profile revealed high rates of N and S transformations via abiotic reactions. The river profile showed enhanced abiotic photodegradation of lignin-like molecules that subsequently entered the hyporheic zone as low molecular weight, more degraded compounds. While the compounds in river water were in part bio-unavailable, some were further shown to increase rates of microbial respiration. Together, river water and ground water enhance microbial activity within the hyporheic zone, regardless of river stage, as shown by elevated putative amino-acid transformations and the abundance of amino-sugar and protein-like compounds. This enhanced microbial activity is further dependent on the composition of ground water and river water inputs. Our results further suggest that abiotic controls on DOM should be incorporated into predictive modeling for understanding watershed dynamics, especially as climate variability and land use could affect light exposure and changes to ground water essential elements, both shown to impact the Columbia river hyporheic zone.
Abstract. Surface water quality along river corridors can be modulated by hyporheic zones (HZs) that are ubiquitous and biogeochemically active. Watershed management practices often ignore the potentially important role of HZs as a natural reactor. To investigate the effect of hydrological exchange and biogeochemical processes on the fate of nutrients in surface water and HZs, a novel model, SWAT-MRMT-R, was developed coupling the Soil and Water Assessment Tool (SWAT) watershed model and the reaction module from a flow and reactive transport code (PFLOTRAN). SWAT-MRMT-R simulates concurrent nonlinear multicomponent biogeochemical reactions in both the channel water and its surrounding HZs, connecting the channel water and HZs through hyporheic exchanges using multirate mass transfer (MRMT) representation. Within the model, HZs are conceptualized as transient storage zones with distinguished exchange rates and residence times. The biogeochemical processes within HZs are different from those in the channel water. Hyporheic exchanges are modeled as multiple first-order mass transfers between the channel water and HZs. As a numerical example, SWAT-MRMT-R is applied to the Hanford Reach of the Columbia River, a large river in the United States, focusing on nitrate dynamics in the channel water. Major nitrate contaminants entering the Hanford Reach include those from the legacy waste, irrigation return flows (irrigation water that is not consumed by crops and runs off as point sources to the stream), and groundwater seepage resulting from irrigated agriculture. A two-step reaction sequence for denitrification and an aerobic respiration reaction is assumed to represent the biogeochemical transformations taking place within the HZs. The spatially variable hyporheic exchange rates and residence times in this example are estimated with the basin-scale Networks with EXchange and Subsurface Storage (NEXSS) model. Our simulation results show that (1), given a residence time distribution, how the exchange fluxes to HZs are approximated when using MRMT can significantly change the amount of nitrate consumption in HZs through denitrification and (2) source locations of nitrate have a different impact on surface water quality due to the spatially variable hyporheic exchanges.
Climate change is intensifying the hydrologic cycle, leading to more frequent and severe rainfall-driven (pluvial) flooding in urban areas. In the mid-Atlantic US cities, aging and under-designed stormwater infrastructure is increasingly strained by these events, resulting in recurring damage to property and disruptions to transportation networks. In this study, we combine community engagement with hydrologic modeling to develop and evaluate potential urban flood adaptation strategies. Over a three-year period, local technical experts and community representatives met regularly to discuss flooding concerns, identify priorities, and co-develop adaptation strategies. These discussions informed the development of an urban flooding model (EPA Storm Water Management Model) for the Baltimore Harbor watershed, the focus location of this study. The flooding model integrates complex surface and subsurface stormwater infrastructure data, local expert knowledge, and community insights. We simulate stakeholder-prioritized adaptations, such as green and gray infrastructure strategies. Model results demonstrate that enhanced infrastructure maintenance is the most effective adaptation for reducing flood depths, but has varied effects across the watershed, and can increase flooding in some locations. Spatially concentrated greening provides limited benefit to the watershed as a whole, but moderate benefit in community priority areas. Together, these adaptations have the potential to reduce flood depths by as much as 58% in some locations, greatly reducing property damage and mobility impacts, primary concerns of stakeholders. Future work will implement robust optimization tools to search for adaptations which meet stakeholder objectives and perform highly under varied future climate conditions. This work contributes to the expanding literature on collaborative modeling and demonstrates that community-engaged approaches can enhance model credibility and generate more actionable insights for communities seeking to strengthen climate resilience.
Climate change is intensifying the hydrologic cycle, leading to more frequent and severe rainfall-driven (pluvial) flooding in urban areas. In the mid-Atlantic US cities, aging and under-designed stormwater infrastructure is increasingly strained by these events, resulting in recurring damage to property and disruptions to transportation networks. In this study, we combine community engagement with hydrologic modeling to develop and evaluate potential urban flood adaptation strategies. Over a three-year period, local technical experts and community representatives met regularly to discuss flooding concerns, identify priorities, and co-develop adaptation strategies. These discussions informed the development of an urban flooding model (EPA Storm Water Management Model) for the Baltimore Harbor watershed, the focus location of this study. The flooding model integrates complex surface and subsurface stormwater infrastructure data, local expert knowledge, and community insights. We simulate stakeholder-prioritized adaptations, such as green and gray infrastructure strategies. Model results demonstrate that enhanced infrastructure maintenance is the most effective adaptation for reducing flood depths, but has varied effects across the watershed, and can increase flooding in some locations. Spatially concentrated greening provides limited benefit to the watershed as a whole, but moderate benefit in community priority areas. Together, these adaptations have the potential to reduce flood depths by as much as 58% in some locations, greatly reducing property damage and mobility impacts, primary concerns of stakeholders. Future work will implement robust optimization tools to search for adaptations which meet stakeholder objectives and perform highly under varied future climate conditions. This work contributes to the expanding literature on collaborative modeling and demonstrates that community-engaged approaches can enhance model credibility and generate more actionable insights for communities seeking to strengthen climate resilience.
This package contains the data, simulation setups, notebooks and figures used in “Modeling the Effects of Wetland Restoration on Coastal Hydrology: A Case Study of Elkhorn Slough Watershed, California” (Xu et al., 2025). In this study, we selected Elkhorn Slough, a tidal estuary, in California, to investigate the impact of wetland restoration and sea level rise on coastal hydrology using the process-based coastal hydrologic model, Advanced Terrestrial Simulator (ATS), informed by site-specific data. We designed a novel modeling workflow for incorporating wetland restoration features into land cover and soil properties for the model parameterization. The validation results demonstrate a strong agreement between modeled and observed data. We studied the characteristics of coastal watershed hydrology, then focused on the surface water dynamics at two wetland sites within Elkhorn Slough, a reference site and a restored site. Our simulation results indicate that the restored site successfully maintains surface elevation, resulting in reduced surface inundation. We also examined the impact of wetland restoration under expected sea level rise over the next few decades. The low-lying Yampah Marsh, the reference site, is likely to be inundated due to future sea level rise when highest tides arrive; while a higher percentage of Hester Marsh, the restored site, would retain marsh vegetation in coming decades, regardless of tidal conditions. Our study provides important information for examining the outcome of restoration practices that include surface elevation in tidal wetlands under climate changes.Several files can be found from this data package.1. README.md: This file describes the title, journal, co-authors, abstract, repository structure and model version.2. Simulation_Setups.zip: The file contains the model configuration files (XML format) for ATS. 3. Notebooks.zip: The file contains the Jupyter notebooks for generating the pre- and post-restoration meshes and the meshes of future scenarios. 4. Figures.zip: The file contains the figures used in the manuscript.5. Data.zip: The file contains the data used to drive the model simulations, including watershed and wetlands boundaries, mesh files and references to additional datasets (e.g., meteorological forcing, tidal dataset, DEMs, land cover, soil properties). Also, it contains water level observations at the restored wetland.
Considerable advancement in spatiotemporal resolution of remote sensing and ground-based measurements has enabled refinement of parameters used in land surface models for simulating surface water fluxes. However, land surface modeling capabilities are still inadequate for accurate representation of subsurface properties and processes, which continue to limit the accuracy of land surface model simulation. Our objective in this study was to examine the performance of the variously parameterized Noah-Multiphysics (Noah-MP) land surface model and to improve simulations of evapotranspiration (ET) and soil moisture dynamics in stony soils using verification from eddy covariance ET and in-situ soil moisture data. Meteorological and eddy covariance data from the Lower Sheep sub-catchment within the Reynolds Creek Experimental Watershed in Southwestern Idaho were employed to drive Noah-MP and to assess simulation results. We evaluated the performance of Noah-MP considering four different scenarios: (1) A one-layer soil profile with Noah-MP default soil hydraulic parameters, followed by five-layer soil profiles using -(2) Noah-MP default soil hydraulic parameters -(3) soil hydraulic parameters derived from a pedotransfer function using field observations, and -(4) hydraulic parameters from (3) which also accounted for stone content in each layer. Each modeling experiment was forced with the same set of initial conditions, atmospheric input and vegetation parameters. Our results indicated that enhanced representation of soil profile properties and stone content information noticeably improve the Noah-MP land surface model simulation of soil moisture content and evapotranspiration.
This data package contains numerical simulation results of surface flow variables such as flow velocity and water depth in Lower Triangle Region in East River Watershed, Colorado. The surface flow is a consequence of a high intensity rainfall event with a total duration of 3 days, available at a resolution of 10 minutes. The results are computed on triangular multiresolution meshes with resolutions ranging from 10 meter to 80 meter. The data package also contains a simulation on a uniform triangular mesh with a resolution of 10 meter. The simulations consider surface flow only and neglect subsurface flow, infiltration, and evapotranspiration. The purpose of the data is to assess the quality of a mesh refinement strategy.
The 2020 Multiscale Microbial Dynamics course is adapted from the virtual 2020 Mutliscale Microbial Dynamics Summer School that was hosted by Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy (DOE) science user facility located on the Pacific Northwest National Laboratory (PNNL) campus, in collaboration with the Joint Genome Institute (JGI) and the DOE Systems Biology Knowledgebase (KBase). The course course covers how to incorporate microbial metagenomic and environmental metabolite data from watershed ecosystems into metabolic and community modeling using computational frameworks, such as KBase and PFLOTRAN. The curriculum includes lectures and software and data analysis tutorials. All materials are freely accessible to the community as part of the 2020 Microbial Dynamics Summer School Organization in KBase.
Model selection for water quality forecasting depends on many factors including analyst expertise and cost, stakeholder involvement and expected performance. Water quality forecasting in arid river basins is especially challenging given the importance of protecting beneficial uses in these environments and the livelihood of agricultural communities. In the agriculture-dominated San Joaquin River Basin of California, real-time salinity management (RTSM) is a state-sanctioned program that helps to maximize allowable salt export while protecting existing basin beneficial uses of water supply. The RTSM strategy supplants the federal total maximum daily load (TMDL) approach that could impose fines associated with exceedances of monthly and annual salt load allocations of up to $1 million per year based on average year hydrology and salt load export limits. The essential components of the current program include the establishment of telemetered sensor networks, a web-based information system for sharing data, a basin-scale salt load assimilative capacity forecasting model and institutional entities tasked with performing weekly forecasts of river salt assimilative capacity and scheduling west-side drainage export of salt loads. Web-based information portals have been developed to share model input data and salt assimilative capacity forecasts together with increasing stakeholder awareness and involvement in water quality resource management activities in the river basin. Two modeling approaches have been developed simultaneously. The first relies on a statistical analysis of the relationship between flow and salt concentration at three compliance monitoring sites and the use of these regression relationships for forecasting. The second salt load forecasting approach is a customized application of the Watershed Analysis Risk Management Framework (WARMF), a watershed water quality simulation model that has been configured to estimate daily river salt assimilative capacity and to provide decision support for real-time salinity management at the watershed level. Analysis of the results from both model-based forecasting approaches over a period of five years shows that the regression-based forecasting model, run daily Monday to Friday each week, provided marginally better performance. However, the regression-based forecasting model assumes the same general relationship between flow and salinity which breaks down during extreme weather events such as droughts when water allocation cutbacks among stakeholders are not evenly distributed across the basin. A recent test case shows the utility of both models in dealing with an exceedance event at one compliance monitoring site recently introduced in 2020.
Hydrologic predictions at rural watersheds are important but also challenging due to data shortage. Long short-term memory (LSTM) networks are a promising machine learning approach and have demonstrated good performance in streamflow predictions. However, due to its data-hungry nature, most LSTM applications focus on well-monitored catchments with abundant and high-quality observations. In this work, we investigate predictive capabilities of LSTM in poorly monitored watersheds with short observation records. To address three main challenges of LSTM applications in data-scarce locations, i.e., overfitting, uncertainty quantification (UQ), and out-of-distribution prediction, we evaluate different regularization techniques to prevent overfitting, apply a Bayesian LSTM for UQ, and introduce a physics-informed hybrid LSTM to enhance out-of-distribution prediction. Through case studies in two diverse sets of catchments with and without snow influence, we demonstrate that 1) when hydrologic variability in the prediction period is similar to the calibration period, LSTM models can reasonably predict daily streamflow with Nash–Sutcliffe efficiency above 0.8, even with only 2 years of calibration data; 2) when the hydrologic variability in the prediction and calibration periods is dramatically different, LSTM alone does not predict well, but the hybrid model can improve the out-of-distribution prediction with acceptable generalization accuracy; 3) L2 norm penalty and dropout can mitigate overfitting, and Bayesian and hybrid LSTM have no overfitting; and 4) Bayesian LSTM provides useful uncertainty information to improve prediction understanding and credibility. In conclusion, these insights have vital implications for streamflow simulation in watersheds where data quality and availability are a critical issue.
Due to the nature of nitrogen cycling, policies designed to address water quality concerns have the potential to provide benefits beyond the targeted water quality improvements. For example, actions to protect water quality by reducing nitrate leaching from agriculture also reduce emissions of nitrous oxide, a potent greenhouse gas. These positive effects, which are incidental to the regulation's intended target, are termed “co-benefits.” To quantify the co-benefits associated with reduced nitrate leaching, we integrate an economic model of farmer decision making with a model of terrestrial nitrogen cycling for the watershed surrounding Lake Mendota, Wisconsin, USA. Our modeling approach provides a framework that links air and water pollutants in an agri-environmental system and offers a direction for future studies. Our model results highlight the finding that the co-benefits from nitrous oxide abatement are substantial, and their inclusion increases the benefit–cost ratio of water quality policies. Consideration of these co-benefits has the potential to reverse the conclusions of benefit–cost analysis in the assessment of current water quality policies.
There is a growing understanding of the role that bedrock weathering can play as a source of nitrogen (N) to soils, groundwater and river systems. The significance is particularly apparent in mountainous environments where weathering fluxes can be large. However, our understanding of the relative contributions of rock-derived, or geogenic, N to the total N supply of mountainous watersheds remains poorly understood. This dataset contains model output from the High-Altitude Nitrogen Suite of Models (HAN-SoMo), a watershed-scale ensemble of process-based models to quantify the relative sources, transformations, and sinks of geogenic and atmospheric N through a mountain watershed. Our study is based in the East River Watershed (ERW) in the Upper Colorado River Basin. The East River is a near-pristine headwater watershed underlain primarily by an N-rich Mancos Shale bedrock, enabling the timing and magnitude of geogenic and atmospheric contributions to watershed scale dissolved N-exports to be quantified. Six calibration scenarios were developed to explore equifinality using >1600 N concentration measurements from streams, groundwater, and vadose zone samples collected over the course of four years across the watershed, from 2014-2018. The files in this dataset are named according to which calibration scenario they represent (1, 2, 3, NM1, NM2, and NC), and include daily time series model output of nitrate, ammonium and dissolved organic nitrogen concentrations for all six calibration scenarios described in Maavara et al., 2021, "Modeling geogenic and atmospheric nitrogen through the East River Watershed, Colorado Rocky Mountains," PLOS One (in press), for the stream, vadose zone, and groundwater in the five discretized subwatersheds: Rustlers Gulch, Copper Creek, East above Quigley (EAQ), the Middle East River (ME), and Lower Triangle (LT) from Gothic to the Pumphouse. The READ_ME.txt file includes details on units and naming conventions in each of these files. Model files are in .mat format, to be opened in MATLAB.
Nutrient exports from agricultural lands in the Great Lakes Region pose significant threats to water quality and ecological health through eutrophication, hypoxia, and harmful algal blooms. Climate change and agricultural adaptation practices complicate future nutrient loading due to intensified hydrologic cycles and land use decisions. Our research focuses on evaluating the Soil and Water Assessment Tool (SWAT) plus model parametric uncertainties for human and natural outcomes across different scales. These factors are integral to ensuring a balance between productive agricultural practices and maintaining the health of watershed hydrology. However, uncertainties in modeling such complex interactions pose significant challenges, limiting our ability to precisely determine critical factors that influence crop yield and soil moisture. Our analysis employs Sobol global sensitivity analysis to evaluate first-order, second order, and total-order indices for SWAT crop growth parameter, ensuring comprehensive assessment of individual and interactive effects on model outputs. The objective is to identify the parameters that significantly affect model outputs for crop yield and soil moisture and improve our understanding of their interactions at the basin and hydrological response unit (HRU) scale. Our case study, the Portage River Watershed, which drains into Lake Erie, is chosen to better capture finer scale interactions crucial for predicting nutrient loading under future climate scenarios. This foundational work is aimed at setting the stage for the future development of an agent-based model (ABM). The ABM model would incorporate SWAT outputs to dynamically simulate decision-making processes.
Our project aimed to guide the representations of peatland hydrology and water-carbon feedbacks within Earth System Models, by improving process understanding and developing parsimonious models that elucidate the effects of hydroclimatic variability and spatial heterogeneity. Our research questions centered on the three key drivers of peatland hydrology: (1) seasonal and interannual hydroclimatic fluctuations, (2) spatial heterogeneity of peatland microtopography, and (3) hydrological connectivity across landscape units within a peatland watershed. Our analyses and model testing used existing long-term datasets within the Marcell Experimental Forest (MEF), with new data collected whenever necessary. To date, we have demonstrated the strong influence of water table elevations on the temperature sensitivity of CH 4 emissions, using a newly developed eddy covariance dataset spanning eleven years at MEF. Specifically, higher water tables dampen the increase in CH 4 emissions in the spring as well as their decrease in the fall, resulting in hysteresis. These results imply that any hydroclimatological changes in peatlands that shift seasonal water availability from winter to summer will increase annual CH 4 emissions, even if soil temperature remains unchanged. To further investigate water table elevation change within the peatland microtopography, we installed automated water table gauges across four bog-forest transects (the “lagg”) in two peatland watersheds at MEF, which are hotspots of intense biogeochemical activity. These measurements will give us new information about the extent of lagg expansion and contraction during snowmelt and high intensity rainfall events, as well as the directionality of water and nutrient flow into the bog from the surrounding forests. Finally, we investigated the hydrological connectivity across the peatland watershed complex during early spring – a critical period where water table is elevated from snowmelt – using extended hydrological records from MEF (e.g., snow and frost depths, water table elevations, streamflow). The importance of thermal and wintertime processes within the Energy Exascale Earth System Model (E3SM) was determined through sensitivity analyses. Results from data analyses show that (i) streamflow has decreased over decades likely due to increased evapotranspiration rates (despite no detectable trends in precipitation), (ii) spring streamflow generation is controlled by a sequence of fill-and-spill pathways from the snowpack to the stream through peatland water stores, and (iii) frost depth is a key explanatory variable for the timing and magnitude of streamflow. These results suggest that frost plays an important role in connecting surface water storage in peatlands to stream outlets, and that the hydrological connectivity across the peatland watershed complex can mediate the sensitivity of hydrological responses to climate variations.
Abstract Climate change and other disturbances significantly impact hydrogeochemical exports from mountainous headwater catchments such as the Upper Colorado River Basin. Developing a mechanistic understanding of how the physical and chemical processes interact in time and space in an integrated manner is key to quantifying the future impacts of such disturbances. The hydrogeochemical response of a mountainous catchment in the 2010–2019 period is evaluated quantitatively using a high‐resolution model that simulates integrated hydrology, and transport and reactions for selected solutes and minerals. The model assumes that pyrite is present only at depth while calcite is distributed uniformly, and captures the observed C‐Q reasonably well. Distinct C‐Q dynamics are observed in an average (WY16), a wet (WY17), and a dry (WY18) water year. The model also quantifies the water fraction from surface, shallow and deep groundwater compartments using tracers, and suggests greater groundwater contributions to peak stream discharge in the dry WY18. Results demonstrate that calcium concentrations do not change significantly from year to year, while sulfate shows significant temporal variability. Pyrite dissolution is affected by the changing hydrological drivers where it is enhanced in the dry WY18; calcite dissolution supplements calcium dilution under high flow conditions. The model simulates the reaction hotspots controlled by hydrological conditions, and the spatially‐resolved results show that higher soil saturation and less snowpack occur earlier on the south‐facing side than on the north‐facing side. This is a first‐of‐its‐kind demonstration of a model that integrates hydrologic processes, including evapotranspiration, and reactive transport to enable a predictive understanding of hydrogeochemical exports.