The present study aims to evaluate the potential effects of cyanobacteria on water quality parameters and Oreochromis niloticus in the fish ponds at Al-Abbassa Fish Hatchery, Sharkia Governorate, Egypt. The study identified five cyanobacterial genera: namely, Anabaena, Gleotrichia, Lyngbya, Oscillatoria and Phormidium. Oscillatoria sp. was the dominant genus in the selected fish ponds. Physico-chemical parameters of water samples showed significant variations during the four seasons. Anabaena sp. extract had the most toxic effect on the survival rate of O. niloticus after 72 h of exposure. Biochemical parameters of collected O. niloticus fish significantly increased compared to the control group. We concluded that the detected cyanobacterial genera in the fish ponds affected water quality and O. niloticus fish. © 2022 Informa UK Limited, trading as Taylor & Francis Group.