New Model Shows Hydrologic Exchange is Primarily Controlled by the Thickness of Permeable Sediments along the River Bank

Novel 3D groundwater model reveals roles of dynamic flow conditions, river morphology, subsurface hydrogeology in controlling hydrologic exchange flows.

The Science

Hydrologic exchange flows (HEFs) between groundwater and river water increase the contact between river water and subsurface sediments, and thereby play a critical role in biogeochemical and ecological functions along river corridors. In a recent paper led by Pin Shuai and Xingyuan Chen at Pacific Northwest National Laboratory (PNNL), a multi-institutional team of researchers found that the dominant factors controlling the hydro-geochemical signatures of HEFs along a dam-regulated river reach are river channel morphology and a river channel’s subsurface hydrogeology. These features were found to control the locations of high exchange flow rates—that is, likely “hot spots” of biogeochemical activity. They also found that the magnitude and timing of river stage fluctuations, caused by dam operations, controlled hydrological “hot moments,” of the timing of when biogeochemical activity was likely to be high.

The Impact

This research improves scientific understanding of hydro-geomorphic controls on HEFs at river-reach scale under high-frequency flow variations, an important issue in an era of increased worldwide interest in building hydropower dams. The paper also demonstrates the influences of river water intrusion on the migration of groundwater contaminant plumes—particularly for contaminant sources located within the preferential flow path shaped by ancient, deep river remnants called paleochannels. Importantly, the paper’s modeling approach and main findings are transferrable to other river corridor systems that experience regular, periodic fluctuations.


HEFs across the interface of a river and its aquifer have important implications for biogeochemical processes and for contaminant plume migration in river corridors, including those that are increasingly regulated by dams across the world. Yet little is known about the hydro-geomorphic factors that control the dynamics of HEFs under dynamic flow conditions.

To help close that knowledge gap, this follow-up study to Song et al. 2018 expands the model domain from a 2D transect to a simulated 3D river corridor. In this new paper, the modeling domain now covers the entire Hanford Reach of the Columbia River. The results demonstrate large spatial and temporal variability in exchange flow magnitude and direction in response to dynamic river flow conditions. The study also highlights the role of upstream dam operations in enhancing the exchange between river water and groundwater. In turn, that enhanced exchange posits a strong potential influence on associated biogeochemical processes and on the fate and transport of groundwater contaminant plumes in river corridors.

This is the first study to mechanistically simulate, at relatively fine resolution, reach-scale hydrologic exchange as it is influenced by dynamic river-stage variations, channel morphology, and subsurface hydrogeology. Because of complex geologic and dynamic flow boundary conditions, the authors faced a great challenge in running their large numerical model (60 x 60 km) using relatively fine model resolution.

However, they were able to develop a large groundwater model using PFLOTRAN, developed by the U.S. Department of Energy (DOE), a next-generation, massively parallel, reactive flow and transport simulator. This scheme, typically employed to simulate the migration of contaminants in groundwater, enabled researchers to use reasonably fine grids (100 m horizontally and 2 m vertically), while at the same time simulating the complexity of a large field setting. To perform their simulations, the researchers employed resources from the National Energy Research Scientific Computing Center.

In all, the PNNL-led research aligns with DOE’s mission to provide next-generation science-based models of watershed systems. The next step, already underway, is to study the effect of dam operations on river corridor thermal regimes and the resulting implications for river ecology.

Principal Investigator

Xingyuan Chen
Pacific Northwest National Laboratory
[email protected]

Program Manager

Paul Bayer
U.S. Department of Energy, Biological and Environmental Research (SC-33)
Environmental System Science
[email protected]


This research was supported by the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE), as part of the Subsurface Biogeochemical Research Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL). PNNL is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RL01830. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231.


Shuai, P., X. Chen, X. Song, G.E. Hammond, J. Zachara, P. Royer, H. Ren, W.A. Perkins, M.C. Richmond, and M. Huang. "Dam Operations and Subsurface Hydrogeology Control Dynamics of Hydrologic Exchange Flows in a Regulated River Reach." Water Resources Research 55 (4), 2593–2612   (2019).