Subsurface Biogeochemical Research. Click to return to home page.
Department of Energy Office of Science. Click to visit main DOE SC site.

Subsurface Biogeochemical Research Program

River Corridor and Watershed Hydrobiogeochemistry Scientific Focus Area

Developing a predictive understanding of hydrologic exchange flows and their influence on river corridor and watershed function.

Principal Investigators: Tim Scheibe, Xingyuan Chen, and James Stegen

Hyporheic zone Columbia River Field Site. The Hanford Reach is a 70-km stretch of the Columbia River. It is bordered by agriculture on the east and north and the Hanford site on the west and south. It has many islands, an active riparian zone, and complex channel physiography. Click image to enlarge.

Exchange of water between rivers and the surrounding subsurface environments is a vital aspect of watershed function. These hydrologic exchange flows (HEFs) lead to enhanced biogeochemical activity (accounting for up to 96% of respiration within river ecosystems) and modulate water temperatures, thus playing a key role in water quality, nutrient dynamics, and ecosystem health. However, these complex processes are not well understood, particularly in the context of large managed rivers with highly variable discharge, and are poorly represented in system-scale computational models. A Scientific Focus Area (SFA) project led by Pacific Northwest National Laboratory (PNNL) is addressing these challenges. The project is supported by the Department of Energy's (DOE) Office of Biological and Environmental Research (BER) as part of BER's Subsurface Biogeochemical Research (SBR) program.

The project's field site is a free-flowing section of the Columbia River (called the Hanford Reach) in eastern Washington state. Research activities are being conducted in the river corridor, which includes the surface water channel and other functionally connected features such as the hyporheic zone, near-shore groundwater aquifer, riparian zone, and vadose zone. The biogeochemical functioning of the river corridor and solute transport both within and through the corridor are controlled by the local groundwater gradient, variable river discharge, subsurface material properties, and river channel morphology. Changes in river discharge occur seasonally (with maximum river stage occurring in spring from snowmelt) and daily (driven primarily by variations in hydropower production at upstream dams). This variable discharge causes fluctuations in river stage (water surface elevation) that control the spatial distribution, magnitude, and direction of HEFs. Consequently, the system's biogeochemistry and ecology are highly dynamic and strongly interconnected with hydrologic processes.

Gas Collection Chamber Hydrologic Exchange Flows. Conceptual river corridor diagram showing various types and scales of HEFs. Click image to enlarge.

Key Scientific Questions

PNNL SBR SFA researchers are developing mechanistic understanding of coupled hydrologic and biogeochemical processes in large, dynamic rivers and associated watersheds and translating that understanding into multiscale numerical models.

Key questions include:

  • What are the hydrobiogeochemical processes that link river stage fluctuations and hydromorphic and hydrogeological setting to distributions of HEFs, residence times, and reaction rates?
  • What are the manifestations of mechanistic processes at larger scales, and what is the appropriate representation of fundamental processes in system-scale predictive hydrobiogeochemical models?

Translating Process Understanding Across Scales

Biogeochemical reaction network Linking Across Scales. Research activities are designed to translate the effects of coupled hydrobiogeochemical processes at the local scale to predict their cumulative impact at reach and watershed scales. Click image to enlarge.

SFA research includes fundamental process identification and quantification, integration of modeling and experimentation at multiple physical scales, and implementation of a novel and computationally efficient multiscale modeling framework. This framework incorporates new process understanding into local-scale, high-resolution mechanistic models, which, in turn, are used to formulate simplified (reduced-order) models applicable at system scales. Accordingly, research activities are organized and integrated around process studies, mechanistic models, and system models.

Process studies advance state-of-the-science hydrobiogeochemical process understanding across scales. This activity emphasizes field observations and experiments in the river corridor to study the effects of variable river discharge on key biogeochemical and ecological processes.

Mechanistic models apply new process understanding to elucidate mechanisms and characteristic component behaviors. This activity emphasizes high-resolution, local (km-scale and smaller) numerical models in the river corridor.

System models develop and link reduced-complexity model components to understand and predict system responses to natural and anthropogenic perturbations. This activity emphasizes reach- and watershed-scale numerical model development and integration.

Toward Predictive Understanding

The PNNL SBR SFA aims to develop a fundamental and comprehensive scientific understanding of HEF influences (particularly those driven by river discharge variations) on river corridor biogeochemical and ecological functions. Findings are integrated into a first-of-its kind hydrobiogeochemical model of the river corridor, which is a critical component of watershed systems models. This new, predictive understanding of HEFs and biogeochemistry in the river corridor will play a key role in reducing uncertainties associated with major Earth system biogeochemical fluxes, improving predictions of environmental and human impacts on water quality and riverine ecosystems, and supporting environmentally responsible management of linked energy-water systems.

Community Engagement

Biogeochemical reaction network Peeper Installation. PNNL SBR SFA researchers work with collaborators from Ohio State University to install instruments that measure the products of biogeochemical reactions in the hyporheic zone. [Courtesy Kelly Wrighton, Ohio State University] Click image to enlarge.

The Hanford Reach is a rich environment for research because of existing extensive and diverse datasets combined with natural and anthropogenic factors driving hydrology and biogeochemistry. Active engagement between PNNL SBR SFA researchers and university and laboratory collaborators is leading to a community of researchers that can more effectively solve scientific challenges.

An example is the Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (WHONDRS;, which is coordinated by PNNL SBR SFA researchers. WHONDRS is a global consortium of researchers aimed at understanding how high-frequency river stage variations influence river corridor function across a wide range of geographical settings. The consortium is developing new instrumentation to estimate HEFs in dynamic rivers and protocols for sample collection that will extend new process understanding to many other systems worldwide.


WHONDRS is a consortium of researchers and other interested parties that aims to understand coupled hydrologic, biogeochemical, and microbial function within river corridors experiencing recurring, episodic, or chronic hydrologic perturbations. (Jan 21, 2019)

An imaging technology that enables researchers—for the first time—to take four-dimensional views of the subsurface was selected as a 2016 R&D 100 Award winner. The technology combines geology, physics, mathematics and chemistry with supercomputer modeling to create four-dimensional images of what’s happening below the surface. E4D-RT was developed by PNNL's Tim Johnson. (Nov 4, 2016)

More videos from PNNL SFA

Subsurface Biogeochemical-Related BER Research Highlights

Submit Research Highlight

Search Submitted Highlights

Now Featuring

Open Watershed Science by Design Workshop Report

October 2019

CESD Strategic Plan 2018

Climate and Environmental Sciences Division (CESD) Strategic Plan 2018 (PDF; 14MB)

Subsurface Biogeochemical Research Overview

November 2019 [PDF]