Biogeochemical controls on natural and anthropogenic groundwater contaminants in California’s Central Valley

Overview: California’s Central Valley (Figure 1) is one of the most productive agricultural regions in the world. To support the agriculture industry, groundwater is heavily pumped from underlying aquifers for crop irrigation and the land surface is fertilized to aid crop growth (DeSimone et al., 2009). Meanwhile, more than one million people in the region relying on groundwater as their primary drinking water source. Human activity has polluted groundwater aquifers, altering their chemistry such that groundwater in many areas of the Central Valley poses a human health hazard and financial burden to municipal water districts. This research will explore natural and human-triggered biogeochemical processes that affect water quality in the Central Valley in an effort to protect human health and food production in the region.

When: July 5 – August 6, 2021

Where: California State University, Fresno, and the surrounding area

WhoEight rising sophomores, and project directors Dr. Brady Ziegler (Trinity University) and Dr. Aric Mine (California State University, Fresno).

Prerequisites and Recommended Courses: This project is highly interdisciplinary in nature, combining aspects of hydrogeology, geochemistry, and microbiology (i.e., biogeochemistry). As such, an outstanding applicant for this project will have taken one or more of the following:

  •  Introductory Geosciences Course(s)
  • General Chemistry (preferably I and II) with laboratory
  • Introductory Biology with laboratory
  • College-level Mathematics (e.g. Calculus, Statistics, Differential Equations)

Expectations and Obligations:

We seek motivated, driven students that are comfortable working independently and that can work and collaborate well with others. You will be expected to take ownership of your project with guidance from the advisors. This entails collecting, organizing, analyzing, interpreting and presenting data in written and oral form.  Students on this project are obligated to:

  1. Participate in all project-related work during the summer (July 15-August 6, 2021)

2. Write a team abstract and present a paper (poster or talk) at the Geological Society of America National Meeting in Portland, Oregon, October 10-13, 2021 (all expenses covered)

Figure 1. Water table contour map (top) showing the elevation of the water table and direction of groundwater flow in the Central Valley. The regional flow across the valley is shown in cross section (bottom); modified from Williamson et al., (1989) and DeSimone et al. (2009).


The Central Valley is a north-south trending basin formed by east-west tectonic extension. The Valley is filled by marine sediments at depth, which are overlaid by alluvial sediments derived from the erosion of the Sierra Nevada (Page et al., 1986; Davis et al., 1959; Olmsted and Davis, 1961). These continental deposits range between 0.5 to two miles in thickness and consist of interlayered clay and sand units that comprise the major aquifer units (Figure 1). Recharge primarily enters the aquifer as runoff from the topographic highs on the valley margins from the adjacent impermeable Sierra Nevada and Coastal Mountains. Regionally, groundwater flows inward to the valley center before discharging into the San Joaquin River system (Williamson et al., 1989), (Figure 1).

In the past century, the primary groundwater concern in the Central Valley has been decreasing aquifer storage capacity due to land surface deformation (subsidence) caused by over-pumping of the aquifer for irrigation (Faunt et al., 2016). High rates of groundwater withdrawal have led to inelastic compression of the clay interlayers in the subsurface due to a loss of fluid pressure. As a result, some parts of the San Joaquin Valley on the southern end of the Central Valley have experienced >8 m decrease in land surface elevation in the past 100 years (0.6 m in the last two years in Corcoran, CA) (NASA MODIS).

Intensive agricultural activity has raised concerns regarding surface and groundwater quality throughout the state. Nitrate (NO3) is commonly applied to the land surface in the Central Valley as fertilizer to increase agricultural yields (Nolan et al., 2014). However, the introduction of NO3 can have unforeseen consequences on water quality. Excess nitrate is linked to nutrient runoff and harmful algal blooms along California’s coastline. In the subsurface, aquifer biogeochemistry shifts promoting the mobilization of redox-sensitive trace elements that naturally exist in sediments derived from the igneous parent material. In this study, we propose to conduct a groundwater quality survey and sediment chemistry analysis to elucidate biogeochemical mechanisms that mobilize natural contaminants (e.g., uranium and hexavalent chromium) into groundwater in, and surrounding, the city of Fresno, California. Elevated concentrations of nitrates and organic contaminants from industrial and agricultural activity in Fresno drinking water wells have raised local concerns regarding human and ecological health as well as municipal water treatment costs.

Overarching research goals and questions

The overarching goal of this project is to better resolve the reaction mechanisms responsible for trace metal mobilization and groundwater contamination in the Central Valley. To achieve this goal, this research project will be the following research questions:

  1. How does groundwater chemistry (electron acceptors, electron donors, redox sensitive trace elements, in particular, U and Cr) vary laterally in the Central Valley?
  2. How does groundwater and sediment chemistry differ between agricultural regions (with high applications of NO3) and non-agricultural regions?
  3. How does the redox state of groundwater and sediments vary with depth through the unsaturated zone, across the water table, and into the saturated zone?
  4. How does the microbial community in aquifers respond to shifts and changes in aquifer chemistry (redox state, nutrient status etc.)? What are the primary microbial metabolisms in subsurface aquifers (sediments and water) and how are they linked to well fouling and trace metal mobilization?

Potential student projects

To address these research questions, we have defined four potential student projects that use a combination of field sampling and laboratory analyses to characterize groundwater chemistry, sediment chemistry and/or mineralogy, and soil microbiology. The nature of this work is highly interdisciplinary and the projects are all strongly linked and will be integrated to best improve knowledge of the processes affecting water quality.

We do not plan to pre-determine which students will pursue which research project. It is our goal that after the first week of training and some field work that we will be able to assign students to the specific projects based on their research interests, background knowledge, and capabilities.

Project 1: Characterization of aquifer sediment chemistry

Project 2: Microbial community analysis in groundwater and aquifer sediments

Project 3: Groundwater survey, chemical analysis, and GIS data compilation

Project 4: High frequency, long-term monitoring of a newly installed well on CSUF campus

Learning outcomes

Students participating in this project will learn to:

  1. Collect field parameters for groundwater samples including pH, dissolved oxygen, specific conductance, and oxidation-reduction potential;
  2. Perform standard field methods for quantifying alkalinity and dissolved iron;
  3. Collect, preserve, and analyze groundwater samples for a variety of constituents, including anions, cations, and dissolved gases;
  4. Assist professional drillers in the collection of vadose zone and saturated zone sediment core;
  5. Provide high-resolution a quantitative chemical and mineralogical analysis of vadose zone and saturated zone sediment using x-ray fluorescence, x-ray diffraction, and SEM-EDS;
  6. Provide high-resolution mechanistic assessments of elements in the solid phase in sediment cores (i.e., cation exchangeable phases, adsorbed phases, sulfide mineral phases, and oxide mineral phases) using sequential chemical extractions techniques;
  7. Perform 16S rDNA extractions to quantify the microbial communities in wells and in subsurface sediments;
  8. Use an integrated approach to combine spatial groundwater chemistry, sediment chemistry, and microbial community data to assess mechanisms NO3, U, and Cr cycling in the Central Valley;
  9. Compile research results into a well reasoned scientific narrative; and
  10. Communicate research results to others through oral, visual, and written means.


The project directors recognize the uncertainty associated with the ongoing COVID-19 pandemic. Below we present two plans for completing the project.

Plan A (students attending CSUF campus during summer 2021)

We plan for this eight-student project to run tentatively from July 5 through August 6, based out of California State University, Fresno. Students will fly to Fresno on the weekend of July 2 and move into on-campus housing at CSUF. Starting July 5, two-to-three days will be dedicated to training in field methods and the overall project objectives. After the training session, we will then participate in a variety of field work, including the installation of a new well on the campus of CSUF, collection of sediment cores, and sampling of public supply wells in coordination with the city of Fresno, and perhaps sampling of residential wells and monitoring wells owned by the California Water Science Center.

After the first ~1.5 weeks, many of the field samples will have been processed in the lab and will be characterized. During this heavily analytical period, a subset of students will search online databases, such as the National Water Quality Assessment (NAWQA) and National Uranium Resource Evaluation (NURE) databases to extract groundwater chemistry data and use geographic information systems to produce spatial distribution maps for groundwater contaminants relevant to the project. Meanwhile, another subset of students will be responsible for regular (daily or every other day) monitoring and sampling of the newly installed well in the CSUF campus. We may have students switch tasks throughout this period so each student participating in the project gets a chance to experience each component of this interdisciplinary research.

During the last week, students will collaborate to write and submit multiple abstracts (actual number to be determined based on analytical results) for posters to be presented at the Geological Society of America meeting in Fall 2021. Students will depart Fresno the weekend of August 6.

Plan B (Project directors collect field samples and send them to commercial labs for analysis)

If by March 1 it appears that Plan A is not viable due to the pandemic, Ziegler will travel to CSUF in spring 2021. The project directors will collect groundwater samples and sediment cores during this period as described in Plan A, and laboratory analyses will be performed by commercial labs. It is our goal to have samples sent to labs by May 1 to ensure enough processing time to so that we can get data to students by the start of the summer research project.

Starting July 5, the project directors will advise students remotely from their homes in much the same way as Plan A. The distinguishing difference between Plan A and Plan B is that students will not get the field and laboratory experience. However, Plan B will give students more time to think critically about the data that have been collected. During this time, students will get a primer on the project and learn fundamental biogeochemical principles to help them interpret their data. Students will then integrate the new groundwater, sediment, and microbiologic data with existing data from NAWQA and NURE. We again will have students work in pairs, with each pair taking ownership of one aspect of the project. We will have frequent large group meetings in which students will provide updates on their individual findings, and we will think critically about how results from each individual project contribute to the overall investigation of trace element cycling in the Central Valley.


In the last week of the research period, students will collaborate with one another with guidance from Ziegler and Mine to write abstracts for the national Geological Society of America Meeting in Portland, Oregon (GSA dates: Oct 10-13, 2021). It is likely that multiple abstracts will be submitted, with a pair of students taking the lead on each abstract, though the other students would likely be co-authors on each project.

Student researchers for the project will travel to GSA, where the primary co-authors of the project will present a poster or talk of their research results. Students will participate in student-focused activities at GSA, many of which encourage students to clarify their education and career plans and establish a network of geosciences professionals. The summer experience and presentation at GSA aim to excite students in the field of research and the pursuit of science, technology, and mathematics careers


Adler, H. H. (1974). Concepts of uranium-ore formation in reducing environments in sandstones and other sediments. In Formation of uranium ore deposits, Proceedings of a Symposium; Athens, May 6-10, 1974, International Atomic Energy Agency, Vienna.

Burow, K. R., Jurgens, B. C., Belitz, K., Dubrovsky, N. M. (2013). Assessment of regional change in nitrate concentrations in groundwater in the Central Valley, California, USA, 1950s-2000s. Environmental Earth Sciences, 69(8), 2609–2621.

Davis, G. H., Green, J. H., Olmsted, F. H., Brown, D. W. (1959). Ground-water conditions and storage capacity in the San Joaquin Valley, California. USGS Water Supply Paper 1469. US Geological Survey.

DeSimone, Leslie A., Pixie A. Hamilton. (2009) Quality of water from domestic wells in principal aquifers of the United States, 1991-2004. USGS Scientific Investigation 2009-1332. US Geological Survey.

Eary, L. E., Rai, D. (1987). Kinetics of chromium (III) oxidation to chromium (VI) by reaction with manganese dioxide. Environmental Science & Technology, 21(12), 1187-1193.

Faunt, C. C., Sneed, M., Traum, J., Brandt, J. T. (2016). Water availability and land subsidence in the Central Valley, California, USA. Hydrogeology Journal, 24(3), 675-684.

Hansen, J. A., Jurgens, B. C., Fram, M. S. (2018). Quantifying anthropogenic contributions to century-scale groundwater salinity changes, San Joaquin Valley, California, USA. Science of the Total Environment.

He, Y. T., Fitzmaurice, A. G., Bilgin, A., Choi, S., O’Day, P., Horst, J., … Hering, J. G. (2010). Geochemical processes controlling arsenic mobility in groundwater: A case study of arsenic mobilization and natural attenuation. Applied Geochemistry, 25(1), 69–80.

Jurgens, B. C., Fram, M. S., Belitz, K., Burow, K. R., Landon, M. K. (2010). Effects of Groundwater Development on Uranium: Central Valley, California, USA. Ground Water, 48(6), 913–928.

Kurttio, P., Auvinen, A., Salonen, L., Saha, H., Pekkanen, J., Mäkeläinen, I., … & Komulainen, H. (2002). Renal effects of uranium in drinking water. Environmental Health Perspectives, 110(4), 337-342.

Langmuir, D. Aqueous Environmental Geochemistry (1997). Prentice Hall: Upper Saddle River, NJ.

McClain, C., Fendorf, S., Johnson, S., Menendez, A., Maher, K. (2019). Lithologic and redox controls on hexavalent chromium in vadose zone sediments of California’s Central Valley. Geochimica et Cosmochimica Acta, 265, 478–494.

Mills, C. T., Goldhaber, M. B. (2012). Laboratory investigations of the effects of nitrification-induced acidification on Cr cycling in vadose zone material partially derived from ultramafic rocks. Science of the Total Environment, 435, 363-373.

Mills, C. T., Morrison, J. M., Goldhaber, M. B., Ellefsen, K. J. (2011). Chromium(VI) generation in vadose zone soils and alluvial sediments of the southwestern Sacramento Valley, California: A potential source of geogenic Cr(VI) to groundwater. Applied Geochemistry, 26(8), 1488–1501.

Nolan, B. T., Gronberg, J. M., Faunt, C. C., Eberts, S. M., Belitz, K. (2014). Modeling nitrate at domestic and public-supply well depths in the Central Valley, California. Environmental Science & Technology, 48(10), 5643-5651.

Nolan, J., Weber, K. A. (2015). Natural uranium contamination in major US aquifers linked to nitrate. Environmental Science & Technology Letters, 2(8), 215-220.

Nriagu, J. O., Nieboer, E. (Eds.). (1988). Chromium in the natural and human environments (Vol. 20). John Wiley & Sons.

Olmsted, F. H., Davis, G. H. (1961). Geologic features and ground-water storage capacity of the Sacramento Valley, California. USGS Water Supply Paper 1491. US. Geological Survey.

Page, R. W. (1986). Geology of the fresh ground-water basin of the Central Valley, California: with texture maps and sections. Professional Paper 1401-C. US Geological Survey.

Rosen, M. R., Burow, K. R., Fram, M. S. (2019). Anthropogenic and geologic causes of anomalously high uranium concentrations in groundwater used for drinking water supply in the southeastern San Joaquin Valley, CA. Journal of Hydrology, 577, 124009.

Weber, K. A., Thrash, J. C., Van Trump, J. I., Achenbach, L. A., Coates, J. D. (2011). Environmental and taxonomic bacterial diversity of anaerobic uranium (IV) bio-oxidation. Applied Environmental Microbiology, 77(13), 4693-4696.

Tessier, A., Campbell, P. G., Bisson, M. (1979). Sequential extraction procedure for the speciation of particulate trace metals. Analytical Chemistry, 51(7), 844-851.

Ure, A. M., Quevauviller, P. H., Muntau, H., Griepink, B. (1993). Speciation of heavy metals in soils and sediments. An account of the improvement and harmonization of extraction techniques undertaken under the auspices of the BCR of the Commission of the European Communities. International Journal of Environmental Analytical Chemistry, 51(1-4), 135-151.