Effect of effluents into rivers is of great economic, environmental and health concern. Chemical fertilizers are used extensively in modern agriculture, in order to improve yield and productivity of agricultural products. However, nutrients, leaching through the soil from agricultural activities, sewerage effluents and runoff from residential areas reaching river water resources are causing serious pollution. The purpose of this study was to determine the impact of effluent discharges on water quality of River Mathioya in Murang’a County, Kenya. Samples were collected upstream and downstream of Murang’a town along the Mathioya River. The pH, dissolved oxygen, electrical conductivity, total dissolved solid, total suspended solids and temperature were determined using the respective meters. Heavy metals were determined using flame atomic absorption spectrometry while sodium and potassium were determined using flame photometry. Nitrates and phosphates were determined using UV/Visible spectrophotometry. Fluoride ion selective electrode was used to determine fluoride. The study has shown that there was considerable amount of heavy metals in the water samples of Mathioya River, though the levels were below WHO maximum permissible levels for zinc 0.05 - 0.08, chromium 0.02 - 0.03, lead was below the limit of detection and copper 0.03 - 0.04 while iron 0.73 - 1.16 and manganese 0.88-2.24 mg/L exceeded this limit. The concentrations of the physicochemical parameters pH 6.94 - 7.76, TDS (37.84 - 54.59 mg/L), TSS (42.78 - 53.84 mg/L), DO (4.75 - 8.27 mg/L) and EC 63.89 - 80.17, nitrates (6.40 - 13.66 mg/L), phosphates (0.29 - 0.91 mg/L) and fluoride (0.68 - 0.88 mg/L).