Informal settlements in urban areas of sub-Saharan Africa often rely heavily on shallow dug wells for their water supply. However, these wells are susceptible to contamination from various sources due to a lack of protection. This study aimed to assess the microbial quality and physicochemical parameters of shallow wells in Moiben Sub-County, Uasin Gishu County. Specifically, the study sought to: (i) determine the level of microbial contamination in shallow wells, (ii) analyze the physicochemical parameters of the water, and (iii) establish the relationship between shallow well water contamination and the distance of the wells from nearby pit latrines. The study population was 62 shallow wells in five zones of the sub-county. Stratified sampling technique was utilized in proportionally sampling wells for examination. Laboratory analysis was conducted to measure microbial indicators like fecal coliforms, E. coli, and total coliforms, and physicochemical parameters like pH, TDS, electrical conductivity, turbidity, nitrates, nitrites, and ammonia. Observational method was utilized to measure the distance of pit latrines from wells. Data was analyzed inferentially through ANOVA, while microbial contamination was quantified using the Most Probable Number (MPN) technique. Findings indicated that there was a significant correlation between distance from the well and microbial contamination (p < 0.001), and 72.8% of microbial contamination was accounted for by distance. Likewise, 98.7% of physicochemical parameter contamination was accounted for by distance. The results point out that shallow wells closer to latrines have greater levels of contamination, above WHO's safe drinking water guidelines. The research emphasizes maintaining a minimum distance of 50 meters between pit latrines and groundwater sources to avert fecal contamination. The final beneficiaries of these results are policymakers, members of the community, and local health administrators, who can use the data to improve public health, sanitation facilities, and water quality in the region