Concentrations of 17 organochlorine pesticides residues (alpha-HCH, beta-HCH, gamma-HCH, deltaHCH, Heptachlor, Aldrin, Endrin, Endosulfan I, Dieldrin, p,p’-DDT, Endosulfan II, p,p’-DDD, Endrin aldehyde, p,p’-DDE, Endosulfan sulfate, Heptachlor epoxide and Methoxychlor) were analysed in water and sediment from Upper River Kuja catchment, Kenya, between January-October 2015, using GasChromatography (GC) with (GC-ECD) equipment. Nutrient levels and water quality parameters: pH (7.57±0.354), secchi disk (0.05±0.019), dissolved oxygen (DO) (6.96±0.897), temperature (25.39±2.201), conductivity (62.03±23.123) and hardness (26.39±6.063) contributed to significant variations in organochlorine pesticide residue levels observed. Statistical significance differences (p<0.05) between water quality parameters in the sampling stations occurred. Pesticide concentrations ranged within BDL – 0.263µgl-1 , for Heptachlor, BDL – 0.506 µgl-1 Heptachlor epoxide, BDL – 0.506 Aldrin, BDL – 0.014 Dieldrin, p,p’-DDT, BDL – 0.644 p,p’-DDE, BDL – 0.176 p,p’-DDD, and BDL – 2.220 methoxychlor. Sediment pesticide residues were higher during rainy period. Results indicate persistent organic pollutants (POPs) exist in our environment, and recent use in sampled area. Increased aquatic monitoring is recommended to detect persistency and changes in target environment.