Physics and Chemistry of the Earth 125 (2022)Climate variability, anthropogenic activities, and hydrological shifts are fueling the nuisance of harmful algal blooms in water bodies. Unfortunately, cyanobacterial harmful algal blooms (CyanoHABs) dynamics have not received much attention in Tanzania. The study aimed to identify and characterize common species of cyano­ bacteria and examine their possible change in composition and succession in the Ngerengere catchment, Morogoro, Tanzania. Water samples from the selected reservoirs were collected quarterly between October 2017 and September 2018 for physico-chemical parameters in situ and in the laboratory. A benchtop FlowCAM was used for the identification of cyanobacteria and compared with the literature and available online databases. Principal component analysis (PCA) was used to examine the association between the physico-chemical variables and meteorological patterns. The study found common CyanoHABs such as Microcystis, Cylindrospermopsis, Anabaena (Dolichospermum), Lyngbya as well as other species such as diatoms and Euglena which are also considered nuisance. Virtually, a colonial cyanobacteria species dominated the fishponds, while Mindu Dam was more of filamentous species. The study suggest that Mindu dam, based on Carlson’s Trophic State Index (TSI), falls under eutrophic while the fishponds were hypereutrophic. Associated physico-chemical conditions, heavy rainfall and prolonged dry conditions influenced cyanobacteria bloom dynamics. The hydrological connectivity between the fishponds and the Mindu Dam poses a threat to public health because a significant population in Morogoro depends on Mindu Dam for domestic water supply. There is a need for the development of a frame­ work for mitigative and adaptive measures in the catchment, especially during pre-and post-occurrence of blooms.