Groundwater Quality: How Microbial “Halos” Spread Through Floodplain Aquifers

Zones of intense microbial activity grow and spread in response to changing environmental conditions.

Diagram of the stratigraphy of a natural floodplain aquifer (left). Accumulation of organic matter and of mineral reaction product (iron sulfide (FeS)) as simulated in the laboratory and numerical experiments (right).

[Courtesy Stanford University.]

The Science

Floodplain groundwater is a critical resource for human activities and ecosystems, though it is increasingly threatened by climate change. While the impact of climate change on groundwater quantity is well documented, its impact on groundwater quality has received far less attention. In this study, researchers showed that changes in the flow rate or chemical composition of groundwater can destabilize sediments rich in organic matter and microorganisms. This process creates zones, or “halos,” of intense microbial activity that further amplify changes in groundwater composition.

The Impact

The availability of groundwater to humans and ecosystems depends on both its quantity and quality. This study documents a cascading environmental mechanism in which change in the circulation of floodplain groundwater causes change in its chemical composition. This study provides a model that can be used as a stepping stone to better predict the impact of climate change on the groundwater resource.


The researchers combined laboratory experiments and numerical simulations to investigate how mixing and reaction zones develop in floodplain aquifers. They built a series of 30 cm-long flow-through column experiments. The columns contained lenses of fine-grained, organic matter-rich sediments embedded inside coarser-grained, organic matter-poor aquifer sand. Both types of sediments were collected from the same floodplain in Wyoming. The arrangement inside the columns mimicked observed depositional patterns. Oxygen-rich artificial groundwater was continuously injected at the columns’ inlets.

The fine-grained lenses released large amounts of particulate organic matter, likely including live microorganisms, that were transported and redeposited in the surrounding aquifer material. These transfers of organic matter sustained the development of secondary zones, or “halos,” of intense microbial activity. The cumulative microbial activity in these halos could exceed the activity inside the lenses by several orders of magnitude due to their larger volume as well as their access to fresh pools of reactants. The impact of these halos on groundwater quality was both immediate (e.g., decrease in oxygen concentration, increase in iron concentration) and long term, with the accumulation of an inventory of mineral reaction products that could be easily remobilized by subsequent environmental changes.

Principal Investigator

Kristin Boye

Program Manager

Jennifer Arrigo
U.S. Department of Energy, Biological and Environmental Research (SC-33)
Environmental System Science


The project was conceived and supported by the SLAC Floodplain Hydro-Biogeochemistry Science Focus Area program, which is supported by the Biological and Environmental Research (BER) Program within the U.S. Department of Energy’s (DOE) Office of Science.


Babey, T., et al. "Simulation of Anoxic Lenses as Exporters of Reactivity in Alluvial Aquifer Sediments." Geochimica et Cosmochimica Acta 334 119–34  (2022).