Groundwater is the major source of drinking water in most rural areas in developing countries. This resource is threatened by the potential presence of faecal bacteria coming from a variety of sources and pollution paths, the former including septic tanks, landfills, and crop irrigation with untreated, or insufficiently treated, sewage effluent. Accurately assessing the microbiological safety of water resources is essential to reduce diseases caused by waterborne faecal exposure. The objective of this study is to discern which are the most significant sanitary, hydrogeological, geochemical, and physical variables influencing the presence of faecal bacterial pollution in groundwater by means of statistical multivariate analyses. The concentration of Escherichia coli was measured in a number of waterpoints of different types in a rural area located in the coast of Kenya, assessing both a dry and a wet season. The results from the analyses reaffirm that the design of the well and their maintenance, the distance to latrines, and the geological structure of the waterpoints are the most significant variables affecting the presence of E. coli. Most notably, the presence of faecal bacteria in the study area correlates negatively with the concentration of ion Na+ (being an indirect indicator of fast recharge in the study site), and also negatively with the length of the water column inside the well.