High levels of plastic pollutants threaten aquatic habitats as the plastic materials are ingested by aquatic organisms as food. This study assessed seasonal variations of microplastics and the water quality of Njoro River and Lake Nakuru. Selected water physico-chemical parameters were measured. Microplastic abundance in the surface water samples in the dry season was recorded as 47–649 MPs 300L−1 for sampling points in Njoro River and 54–508 microplastics (MPs) 300L−1 for Fisher’s Point in Lake Nakuru; an abundance during the rainy season was measured as 8–389 MPs 300L−1 and 28–259 MPs 300L−1 for Njoro River and Lake Nakuru, respectively. Our study observed a significant pattern of microplastics from polymers such as polyethylene (20%), polypropylene (25%), polyester (40%) and polyethylene terephthalate (10%). Salinity ranged between 0.085 to 2.59 ± 0.03 ppt; temperature 23.69–14.22 ± 0.07°C; pH 8.8–9.3; turbidity 13.95−36.03 ± 0.35 NTU; TN 5.9 to 8.57 ± 3.24 mg L−1; TP 7.49−.41 ± 1.84 mg L−1; EC 73.3−533.3 ± 0.64 μs cm−1; and TDS 46.67–243.33 ± 0.11ppm. These ranges were within the standards recommended by WHO and US EPA. Results indicate the possibility for the quantity and mass of plastic particles in Lake Nakuru to surpass that of Njoro River.