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This study aimed to assess the impact of the cage fish farming on the water quality in two selected bays of the Bukavu basin, Lake Kivu; from February to December 2021. Physicochemical parameters including pH, Temperature, EC, TDS, Salinity, DO, Transparency were sampled in situ using a COMBO HI 98129 multi-parameter probe, PCE-PHD1 probe and a Black & White Secchi disk; water at different depths was collected with the aid of a Van-Dorn Sampler; nutrients namely PO43−, NH4+, NO2−, SiO2, and Chl_a were analysed using the UV-VIS spectrophotometer. The results revealed that water pH, temperature, TDS, salinity and transparency significantly (p ≤ 0.05) varied between the selected sites. Water at the cage sites contained significantly (p ≤ 0.05) much higher concentrations of PO3 − 4, NH4+, NO2−, SiO2 and Chl_a than in control site. In overall, these results suggest that cage fish farming changed water quality in the selected bays. Therefore, the study recommends that measures should be taken to regulate cage fish farming and related activities and deforestation around Bukavu basin to avoid advert conditions.