Physicochemical parameters, phytoplankton communities, microcystin (MC) concentrations and potential MC-producing cyanobacteria were investigated in Lakes Natron and Momela, Tanzania. In Lake Big Momela, concentrations of soluble reactive phosphorus, nitrate and ammonia were 7.1, 2.6 and 0.9 μg/L, respectively, while dissolved oxygen, salinity, conductivity and pH were 9.4 mg/L, 19‰, 30 mS/cm and 9.7, respectively. The concentrations of soluble reactive phosphorus, nitrate and ammonia in Lake Natron were 129.4, 8.1 and 58 μg/L, respectively, while dissolved oxygen, conductivity and pH were 8 mg/L, 52 mS/cm and 9.5 respectively. The phytoplankton communities in both lakes were dominated by cyanobacteria, particularly Arthrospira fusiformis. Navicula and Nitzschia diatoms, and Chlorella, Chlorococcum and Scenedesmus green algae were common in Lakes Momela and Natron. Liquid chromatography–mass spectrometry (LC-MS) analysis phytoplankton detected four microcystin variants namely MC-RR, -YR, -LR and -RY. The total MC concentrations in Lake Natron were 0.1–4.5 μg/mL of phytoplankton scum and in Lake Momela were below quantifiable levels. Polymerase chain reaction analysis of phytoplankton revealed presence of Microcystis and the Microcystis mcyB gene in some samples. Finding of potential MC-producing cyanobacteria and MCs in study lakes poses a health risk to Lesser Flamingo which feed on cyanobacteria.Norwegian Programme for Development, Research and Higher Education (NUFU) PRO 07/10224.