The shallow groundwater sources of boreholes and wells form major sources of water for domestic and agricultural uses in rural areas of Kenya. Information on their status is inadequate thus hinder their sustainable management. This study investigated the relationship between land-use types, ground water sources and water quality, specifically water physicochemical parameters and feacal coliforms that were then used to calculate the water quality index (WQI). Thirty-six randomly selected groundwater sources were obtained from four stratified land-use types of forest, tea, coffee, and urban, with 18 samples each collected for either boreholes or shallow wells. The PCA grouped groundwater resources into three groups according to land-use types and sources. Spearman rank correction found nutrient levels of PO4 and NO3 were strongly correlated with turbidity, electric conductivity, total hardness, feacal coliforms and WQI with the same trends observed for wells. An overall one-way ANOVA found all water quality parameters significantly differed between land-use types for both boreholes and wells at p < 0.05. However, further post-hoc multi-comparison analyses using the Tukey test of unequal N showed not all water quality parameters changed significantly between land-use types, especially between forests and other land-use types. Comparisons of water sources (boreholes versus wells) using unpaired t-test showed most water quality parameters were significantly higher in wells than boreholes apart from pH, PO4, chloride (in the forest), dissolved oxygen, total alkalinity, chloride (tea), Chloride (coffee) and (dissolved oxygen, PO4, fluoride (urban). The WQIs calculated without FC classified groundwater sources from good water to unsuitable for drinking whereas those with FCs parameters were all classified as completely unsuitable for drinking. Overall, this study found that a significant percentage of the population in the study area relied on shallow groundwater resources that were experiencing various levels of pollution from human settlements, urbanization, and agriculture. Consequently, there is an urgent need for the County and National governments to promote sustainable management of water resources to ensure healthy and safe water is available to its people for domestic and agricultural use.