<p> Years of conflict, political instability, and national emergencies have left behind very little information on water resources in Liberia, West Africa. This research leverages major ion and trace element analysis, <i> Escherichia coli</i> (<i>E. coli</i>) field tests, and high-throughput sequencing of microbial 16S rRNA genes to address these gaps and develop a comprehensive snapshot of groundwater quality in the region surrounding Monrovia, the capital city. A novel protocol to collect and preserve microbial DNA from groundwater under tropical field conditions lacking a constant source of electricity was employed and yielded high quality DNA sequences of bacterial and archaeal phylogenetic marker genes. </p><p> Multivariate compositional data analysis methods were used to investigate geochemical processes impacting groundwater quality throughout the study area. Low conductivity, low pH groundwaters were found to dominate the system with the majority of geochemical variability in the water samples attributed to surficial inputs both natural and anthropogenic. The implicated low buffering capacity of the groundwater system suggests a high risk associated with mining operations in Liberia. From a public health perspective, nitrate contamination, attributed to widespread but localized infiltration of human and or animal waste/fertilizer(s), was identified as the most important chemical water quality issue. Sulfate was found to be indicative of urban water cycling processes. </p><p> Although nitrate, arsenic, and lead concentrations exceeded WHO guidelines in several wells, <i>E. coli</i> was identified in 39% of all groundwaters analyzed, suggesting fecal contamination as the most significant regional water quality risk to human health. Deeper wells had significantly (p &lt; 0.05) lower probability of <i>E. coli</i> contamination, with no <i> E. coli</i> encountered in any well greater than 22 meters deep. Sequencing of 16S rRNA genes revealed highly variable microbial community compositions. Surficial inputs are suggested as the major drivers of microbial diversity and community composition. Groundwaters that tested positive for <i> E. coli</i> in the field were found to have significantly higher estimates of microbial alpha diversity (p &lt; 0.05) than groundwaters that tested negative. Additionally, nitrate, silica, pH, and several other geochemical constituents were found to be strongly correlated with shifts in microbial community structure. </p><p> The identification of a wide diversity of pathogen-associated bacteria to the genus and species level suggests that microbial contamination is more widespread than indicated by the <i>E. coli</i> field test alone. Results highlight the vulnerability of aquifers in Liberia to contamination and call for an increased investment in the water supply infrastructure and enhanced monitoring of chemical and microbial constituents throughout the country. This work will help the government of Liberia establish baseline water-quality conditions and provides an initial set of water resource databases to improve water-quality monitoring capacity.</p><p>