Anthropogenic activities have accelerated the process of eutrophication and threatened the health of aquatic ecosystems in Lake Baringo basin. This has necessitated the analysis of its spatial variation in its physico-chemical qualities. Physicochemical parameters from 10 sampling sites distributed throughout Lake Baringo catchment. Mean values of temperature were high at the river inlets and Islands compared to the rivers. While pH and Electrical Conductivity (EC) were relatively constant across the sampling points, Total Dissolved Solids (TDS) were high at the inlets and Islands compared to the rivers, Total Nitrogen mg/ (TN), Nitrates (NO3-) Ammonia ( NH3 ), Total Phosphate (TP) Phosphate and Orthophosphate (OP) were relatively higher in the rivers compared to the inlets and Islands. Temperature ranged between (33.8oC) to (21.4 oC), pH (8.88) to (7.18), EC (543 µS/cm) to (224 µS/cm), TDS (433 mg/L) to (181mg/L), salinity (0.2ppt) to ( 0.01ppt), TN (9.98 mg/L ) to (1.32 mg/L), nitrate (5.11 mg/L) to (0.09 mg/L), NH4 (0.77 mg/L) to (0.09 mg/L), TP(2.91 mg/L) to (0.25 mg/L), OP (1.84 mg/L) to (0.09 mg/L). Nitrite values were below the detectable values <0.05. The result of the study revealed that Lake Basin is highly polluted and undergoing drastic eutrophication due to increased nutrient loading resulting in deterioration of the water quality.