Rapid expansion of commercial horticulture production and related activities contribute to declining surface water quality. The study sought to understand the impacts on select rivers in Laikipia and Meru, production hotspots. The specific aims were (1) to identify prevailing surface water quality by examining variations of 14 physico-chemical parameters, and (2) to categorize measured surface water quality parameters into land use types highlighting potential pollutant source processes. Water samples were collected in July and August 2013 along 14 rivers in the study area. The data were analyzed using principal component analysis (PCA) and discriminant analysis (DA). Principal components (PCs) explained 70% of the observed total variability of water quality, indicating a prevalence of heavy metal traces (cadmium, phosphate, and zinc). These were linked to the rigorous use of phosphate fertilizers and copper-based agrochemicals in intensive farming. DA provided four significant (p < 0.05) discriminant functions, with 89.5% correct assignment enabling the association of land use with observed water quality. Concentrations of dissolved solids, electro-conductivity, and salinity spiked at locations with intensive small-scale and large-scale horticulture. Understanding the impacts of intensive commercial horticulture and land use practices on water quality is critical to formulating ecologically sound watershed management and pollution abatement plans.