Makueni County is located in the semi-arid south-eastern Kenya region characterized by unreliable rainfall and limited surface water resources. This necessitates a high reliance on groundwater for domestic and agricultural use. In this paper, we report on the physico-chemical characteristics of 20 drinking water sources (boreholes, shallow wells, streams, and tap water) collected during the dry season (November 2018), the geochemical processes controlling their composition, and their suitability for drinking water and irrigation. Of all the physico-chemical parameters analysed, the concentrations of total dissolved solids, hardness, electrical conductivity, magnesium, calcium, chloride, and fluoride exceeded the permissible drinking water limits set by both the World Health Organization (WHO) and Kenya Bureau of Standards (KEBS) in up to 55% of the samples. The dominant ions reflect the high salinity in the water that ranged from very high to extreme in up to 50% of samples. The northern region shows the highest concentrations of the dominant parameters. The water type is predominantly Ca-Mg-HCO3 with a trend to Ca-Mg-Cl-SO4. Rock weathering and evaporation are suggested to be the primary controls of groundwater geochemical characteristics. High salinity and fluoride, which are associated with reported undesirable taste and gastrointestinal upsets, as well as cases of dental fluorosis are some of the effects of consuming groundwater in the region. These two parameters can be attributed to the weathering of biotite gneisses, granitoid gneisses, migmatites, and basaltic rocks that occur in the area. The high salinity and alkalinity of most of the samples analysed, renders the water unsuitable for irrigation in the study area.