The threat of climate change, rising human population, and food security are some of the issues that need to be addressed urgently. Therefore the objective of this study is to document the species composition of microalgae and its diversity in different stocking densities of catfish in varying weather conditions to minimize water usage and maximize production. Clarias gariepinus with size 10±0.2 cm and 18.5±0.3 g were placed in a poly tank of 300L under sheltered transparent roofing. The experimental setup comprising of a control tank with 25 fishes and covered to prevent microalgal growth, 10, 15, 20, and 25 fishes for treatment 1, 2, 3, and 4, respectively.  Microalgae were sampled every 2 days; different mean light intensity and temperature represent different weather conditions were recorded. The totals of 29 genera 77 species of microalgae within 5 divisions were identified. The most abundant taxa were Chlorophyta (90%). The common genus in all weather conditions were Chlorella, Desmodesmus, Scenedesmus and Selenastrum. Shannon diversity index (H'), Simpson index, evenness, and species richness were diversity indices that ranged from 0.59-2.82, 0.21-0.97, to 0.52-1.04, and 2.01-5.36, respectively. The highest stocking density of catfish (25 catfish; T4) under dry weather conditions also produce the highest diversity indices.