This study aimed to evaluate the influence of agricultural by-products on the proliferation of potentially toxic microalgae in rice-fish farming. For this purpose, an experiment was carried out in rice-fish culture ponds growing Oreochromis niloticus with four dietary treatments: corn bran input (RSM), rice bran input (RSR), mixed by-product input (RPC) and no feed input (RC). Phytotoxic Dinoflagellata and Cyanobacteria from these ponds were collected monthly for six months. A sampling of these microalgae was done by water filtration and scraping of the algal biofilm attached to the submerged parts of the rice stems. In addition, the physico-chemical parameters of the water in these ponds were measured. The analyses recorded a total of 44 phytotoxic microalgal taxa, including 33 Cyanobacteria and 11 Dinoflagellata with eight taxa constant in the ponds. The majority of these taxa are likely to produce hepatotoxins and neurotoxins in the ponds. The absolute density of potentially toxic pelagic microalgae was significantly higher in RPC (15339 to 24450 Individuals/L) than that in RC (5586 to13078 Individuals/L). Moreover, the density of potentially toxic microalgae epiphytic on submerged rice stems was higher in RPC (113.5 to 160.5 Individuals/cm²) than that in RC (85.5 to 115.96 Individuals/cm²). In contrast to other ponds. Anabaena affinis, Microcystis aeruginosa, Peridinium cinctum and Protoperidinium sp. were the most abundant. The use of rice bran and its combination with other agricultural by-products in rice-fish farming results in the proliferation of toxic Cyanobacteria that would be harmful to fish health.