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Subsurface Biogeochemical Research Program

Groundwater Quality Scientific Focus Area

Advancing predictive understanding of hydrologically driven biogeochemical processes controlling water quality

Principal Investigator: John Bargar

Water Cycle Impacts on Biogeochemistry and Groundwater Quality. Groundwater quality is conditioned by “fine-scale” biogeochemical processes (Ångströms to centimeters) as water travels along flow paths (kilometers) within chemically, physically, and biologically heterogeneous sediments. These processes are mediated by hydrological fluctuations, such as rising and falling water tables.

Groundwater is an endangered resource in the western United States. Wet-dry cycles caused by increasingly frequent and prolonged droughts, flooding, and groundwater pumping to meet municipal, energy, and agricultural demands perturb the chemical, physical, and biological cycles occurring in the shallow subsurface. The resulting implications for nutrient and contaminant behavior are profound. Thus, water quality degradation exacerbates water scarcity.

Floodplains in western watersheds are exposed to annual cycles of wetting as snowmelt drives groundwater to rise in the spring, followed by summertime drying through drainage and evapotranspiration. During such so-called “hot moments,” oxygen concentrations and biogeochemical conditions can change dramatically (e.g., from oxic to reducing). These redox changes drive mineral dissolution and precipitation, causing organic carbon, nutrients, and contaminants to be released or sequestered. Consequently, water quality varies with rising or receding water levels. These processes occur as groundwater flows from higher to lower elevations, regionally, conditioning water quality before it discharges to river systems. However, the hydrological-biogeochemical conditions that trigger redox thresholds and water quality changes are not well understood.

To address this challenge, the Groundwater Quality Scientific Focus Area (SFA), led by SLAC National Accelerator Laboratory (SLAC), is studying how the hydrological cycle (wet-dry events) couples to biogeochemical processes and groundwater quality in western U.S. floodplains. 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) activity. In this endeavor, SLAC researchers are focusing on biogeochemical and transport processes that control nutrient and contaminant mobility in shallow alluvial sediments and mediate groundwater quality. Some of these efforts involve monitoring biogeochemical processes at two DOE field sites that exhibit differing precipitation patterns: (1) a uranium-contaminated semi-arid floodplain in Riverton, Wyoming, and (2) lead- and zinc-contaminated montane floodplains near Crested Butte, Colorado. The goal is to identify, interrogate, and mechanistically model critical processes in these subsurface ecosystems, thereby improving BER’s ability to predict groundwater-quality responses to changing rainfall patterns across this important region.

Key Knowledge Gaps

The Groundwater Quality SFA is investigating the coupling of fine-scale hydrological and biogeochemical processes in transiently saturated zones to understand the implications for groundwater quality. Annual spring-summer wet-dry cycles provide opportunities to study hydrologicalbiogeochemical transitions. Specific questions include:

  • Which parameters accurately predict the onset of redox reactions?
  • How are nitrogen-cycling microbial communities impacted by redox transitions?
  • Which soil and sediment zones dominate chemical inputs to groundwater during different hydrological events (and seasons)?
  • Which organic and mineral phases release contaminants under changing hydrological conditions?
  • How do plant roots influence the organic and mineral phases that host contaminants?
  • Is colloidal transport important at various hydrological and biogeochemical conditions?

Fine-Scale Perspective

Particularly important are contaminant and nutrient processes occurring at the molecular (Ångström) to centimeter scale. Transformations occur at this scale during dissolution of minerals, release of trapped organic matter and heavy metals, redox reactions, and colloid formation. SLAC researchers are using synchrotron-based X-ray absorption spectroscopy at the Stanford Synchrotron Radiation Lightsource (SSRL), high-resolution mass spectrometry, X-ray microscopy, electron microscopy, isotope microscopy, and isotope systematics to identify thermodynamic controls, reaction pathways, and networks. Microbial metabolism and transport of reactants between areas of biogeochemical activity (e.g., saturated and unsaturated zones) occur across scales, from micrometers and soil pores to sediment zones. Metagenomic and transcriptomic approaches are helping the team to decipher how metabolic reactions and microbial community dynamics are linked to geochemical reactions and respond to hydrological perturbations.

Modeling Redox Thresholds

Understanding the key parameters controlling how, when, and where wet-dry cycling drives redox transitions is crucial. SLAC SFA researchers are using a combination of field observations and laboratory experiments to examine how changes in soil moisture influence the molecular forms of key elements and their subsurface behavior, such as partitioning between solid phases and solution. By elucidating key reaction networks and incorporating them in quantitative process representations, researchers can use reactive transport models to understand nutrient and contaminant behavior in these complex systems. Observations of geochemical and microbial dynamics across scales in response to hydrological transitions are critical for improving knowledge of the key parameters required to model groundwater quality.

Linking to Other BER Model Frameworks

Conceptual and quantitative process models developed by the Groundwater Quality SFA complement and feed into watershed hydrological model frameworks developed by other SBR SFA programs, including those at Pacific Northwest National Laboratory and Lawrence Berkeley National Laboratory. Detailed understanding of biogeochemical processes and building representative reaction networks across scales are improving the ability to mechanistically link the water cycle to nutrient and contaminant mobility in the shallow subsurface. Coupling these processes to landscape hydrological transport models will enhance overall model fidelity for predictions of contaminant and nutrient transport to groundwater and to rivers and downstream recipients throughout the water cycle.

Linking Biogeochemistry to the Water Cycle Across Hydrological Zones. In four coupled subtasks, the Groundwater Quality SFA is using field investigations and laboratory experiments to generate fundamental knowledge about what controls biogeochemical responses to hydrological changes and their impact on contaminant and nutrient transport. The goal is to develop quantitative process knowledge that supports landscape-scale hydrological and reactive transport modeling in the SBR program.


John Bargar (Stanford Synchrotron Radiation Lightsource, SSRL) shows how an X-ray microprobe at SSRL beam line 2-3 can be used to develop water quality models to help manage water quality and predict our nations water availability. (Jan. 22, 2018)

Video interview with John Bargar (SLAC National Accelerator Laboratory) describing work being performed within the greater East River Watershed associated with the DOE-funded Groundwater Quality Science Focus Area (SFA) research program, which examines hydrologically driven biogeochemical processes that control water quality. (Dec. 6, 2017)

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