Aquatic ecosystem species are expected to be impacted by climate change. In Africa, conditions that may affect how aquatic species adapt are poorly understood and challenging to predict. In this study, we investigated the possible distribution of three Azolla aquatic fern species in Africa under several scenarios of future climate change. The three species' ecological niche models were developed using MaxEnt using occurrence data and environmental factors. AUC and TSS values for all models were reasonable and above 0.801, suggesting high prediction precision. The results suggested that the major determinant factors restricting the species' future range expansion were elevation and precipitation. Furthermore, we detected notable differences in the three species' unique climatic niches and suitable places. The species' current probable distribution areas ranged from 2,328,726 km2 to 4,026,363 km2. The range of the Azolla species may have extended beyond the known and recorded places, but under future temperature conditions, the species was predicted to lose between 8.1% and 48% of their suitable habitats as a result of climate change. Our findings can be used to devise aquatic species conservation programs that are sustainable and to inform people about the consequences of climate change.