Abstraction Method Shapes Microbial Ecology and Pathogen Risk in Water from Shallow Aquifers

Shallow groundwater is a key water source in semi-arid regions because it can be naturally filtered and stored in riverbeds, protected from evaporation, and accessed year-round. Water harvesting structures are widely built in rural Kenya to improve groundwater availability, but many communities still face a high burden of waterborne disease. One major knowledge gap is how microbial communities behave inside these aquifers and how pathogens enter water that should be naturally protected.This study investigates the microbial ecology of shallow sand dam aquifers in southeast Kenya in order to understand how water abstraction methods affect water quality. Sampling was carried out across multiple seasons and water sources, including sealed hand pumps (classified by WHO as improved sources), open wells, scoop holes, and downstream surface water.Our results show that ecological selection pressures and exposure pathways strongly shape microbial communities in shallow aquifers. Practically, they demonstrate that sand dams can provide safer water, but only if paired with sealed, well-maintained hand pumps. Identified contamination routes highlight where infrastructure upgrades and ongoing maintenance are needed to reduce disease risks.This study contributes new data on groundwater microbiology in low-income, water-scarce regions. It combines ecological theory with molecular tools to explain why some groundwater sources remain safe while others become contaminated. The findings support the use of sealed hand pumps as a cost-effective and sustainable strategy to improve drinking water safety in semi-arid areas, providing evidence to guide both local interventions and broader water policy.