Narok and Bomet are agricultural counties in Kenya which depend on flowing surface waters for farming activities. Agrochemicals have frequently been used to increase agricultural produce in this region. Occasionally, appropriate pesticide utilization measures are not followed. These surface waters are also consumed domestically by humans, livestock, and wild animals thus posing safety concerns to them. The current study sought to evaluate the levels and nature of pesticide residues found in surface waters in the dry and wet seasons of these counties. Eight water samples were collected in July (dry season) and October (wet season) at four different river sites in each of the two counties predetermined by the agricultural activity of its proximate environs. Pesticides extracted by solid phase extraction were analyzed by gas chromatography-mass spectrometry. At least 38 different pesticides were detected in the two counties with the highest concentration being recorded for chlorpyrifos and piperidine in Narok and Bomet counties, respectively. The pesticides chlorpyrifos, cypermethrin, cyfluthrin, and cyhalothrin were more prevalent in Narok County while triazine, semicarbazone, and epinephrine were more prevalent in Bomet County. There were significantly more pesticides detected during the wet season (P ≤ 0.05). Out of the nine prevalent pesticides detected, four of them posed serious ecotoxicology concerns with risk quotients above 1.0 (high risk); thus, there is a need for more government policy interventions in deterring farming near riparian lands and in training of famers regarding best practice for pesticide applications.