Globally, parasitic infections hinder aquaculture productivity and sustainability. Improper water quality parameters reduce fish immunity, make them susceptible to parasites, and enhance parasitic proliferation in culture systems. Subsequently, this study aimed to determine the prevalence and intensity of ecto‐ and endo‐parasite infesting Oreochromis niloticus in varying water quality in aquaculture systems in Kericho, Bomet, and Nakuru counties. A total of 220 Oreochromis niloticus samples were captured from 11 liner ponds, eight earthen ponds, two concrete ponds, and one plastic tank from 22 farms in the three counties. External and internal organs were examined for parasite infestation. Skin scrapings and squash preparation of fish eyes were also examined to reveal the organisms through microscopic examination. A Pearson’s correlation analysis between physicochemical parameters and parasitic prevalence was used to determine the strength and direction of correlation coefficients with significance at 95%. Overall parasitic prevalence infestation was 39.6% (87/220). Ten parasite genera were recovered, with Dactylogyrus species dominating overall at 15.9% (35/220), followed by Trichodina spp. (7.7%; 17/220). Epistylis species had the highest mean intensity of 12.8 ± 35.7 (total number of Epistylis parasites (141)/total of infested fish (11)). Earthen ponds had a significantly higher (36.2%, 29/80) prevalence of Dactylogyrus sp. than liner ponds (3.6%, 4/110) (p < 0.001). Dissolved oxygen levels were 16.9 ± 0.7 mgL−1 in Bomet, 14.9 ± 0.3 mgL−1 in Kericho, and 12.5 ± 0.5 mgL−1 in Nakuru which were above desirable range for fish culture. The electrical conductivity in Bomet was 76 ± 5 µS/cm and Kericho 52 ± 4 µS/cm below the desirable range. Temperature, pH, phosphate, nitrates, and nitrites were within the desirable limit for fish farming. Electrical conductivity and pH had positive correlation of 1 and 0.97, respectively, with the prevalence of Acanthocephalus, Euclinostomum, and Trichodina species. Temperature and nitrate positively correlated between 0.80–0.89 and 0.90–0.99, respectively, with the prevalence of Dactylogyrus, Riboscyphidia, Epistylis, Camallanus, and Paracamallanus species. The study demonstrates that water quality significantly influences parasitic prevalence in aquaculture systems. Therefore, it is crucial for farmers to monitor water quality parameters to mitigate parasitic infestations.
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