Groundwater Quality Science Focus Area


Hydrologically driven biogeochemical processes controlling water quality

The SLAC SFA scientific program addresses the grand challenge: How do biogeochemical and transport processes in shallow alluvial groundwater systems (bedrock to soil) couple to one-another and control water quality under hydrologically variable conditions? We are identifying hydro-biogeochemical mobilization and retention processes for C, nutrients (P, S, and Fe) and contaminants (U, Mo, Pb, Zn) at molecular to meter scales. Emphasis is placed on understanding the spatio-temporal coupling of biogeochemical and hydrological processes in soil, the capillary fringe, and the upper portion of the saturated zone. Field studies at the mining impacted Coal Creek and Slate River head-watersheds (Gunnison county, CO) and the former ore processing site in semi-arid Riverton, WY are combined with laboratory experiments to understand the impact of timing, duration, and intensity of wet-dry cycling, transport direction, organic carbon content and sediment texture on redox and nutrient and contaminant mobilization. Quantitative process representations that are developed within the SLAC SFA program will be shared with collaborating SFAs and the wider community for incorporation into larger-scale models. Results from this work will advance short- and long-term prediction of water quality by DOE and multi-agency collaborations.

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Research highlights

Sorption to Organic Matter Controls Uranium Mobility

Bone SE, Dynes JJ, Cliff J, & Bargar JR “Uranium(IV) adsorption by natural organic matter in sediments.” Proceedings of the National Academy of Sciences of the United States of America 114(4), 711-716. [10.1073/pnas.1611918114]

A new multi-technique study using X-ray absorption spectroscopy at SSRL, nanoscale secondary Ion mass spectroscopy at EMSL, and scanning transmission X-ray microscopy at the CLS has revealed crisp new details about the mechanisms of uranium binding in sediments.  Surfaces of natural organic matter bind uranium more strongly than minerals under field-relevant conditions. Read more >

Thermodynamic preservation of carbon in anoxic environments

Boye, K., Noël, V., Tfaily, M.M., Bone, S.E., Williams, K.H., Bargar, J.R., Fendorf, S. (2017) Thermodynamically controlled preservation of organic carbon in floodplains. Nature Geoscience [10.1038/ngeo2940]

A new study combining X-ray absorption spectroscopy (XAS) at SSRL with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) at EMSL provides new insights on why carbon persists in waterlogged soil and subsurface sediments . Energetic constraints prevent microbial respiration of certain organic carbon compounds, leaving a pool of water-solube carbon that is susceptible to oxidation or export and subsequent decomposition in downstream, aerated environments. Read more >

Combined Fe and S speciation tracks redox conditions in shallow alluvial sediments

Noël V, Boye K, Kukkadapu RK, Bone SE, Lezama Pacheco JS, Cardarelli E, Janot N, Fendorf S, Williams KH, Bargar JR (2017) Understanding controls on redox processes in floodplain sediments of the Upper Colorado River Basin. Science of The Total Environment,

Detailed characterization of the molecular structures of Fe and S, on depth-resolved field samples from floodplain sediments, were performed using x-ray absorption spectroscopy (XAS) and X-ray microspectroscopy at SSRL combined with mössbauer spectroscopy at EMSL. The results revealed that organic carbon content, moisture, and particle size control the distribution and reactivity of redox constraints in the floodplain subsurface. Read more >

Contacts and Websites

Principal Investigator

John Bargar,, (650) 926-4949


This program is funded by the Subsurface Biogeochemistry program within the U.S. Department of Energy, Office of Biological and Environmental Research, Climate and Environmental Sciences Division. Funding for SSRL is provided by the Department of Energy, Office of Basic Energy Sciences.

BER Program Managers

David Lesmes,, (301) 903-2977

Paul Bayer,, (301) 903-5324