The aim of this work is to investigate the effect of exposure of heavy metals such as Ni, Fe and Mn on the growth of the cyanobacteria Anabaena flos-aquae, which can be found in fresh water environment. Results of the experiments showed that exposure of A. flos-aquae to Ni caused the most toxic effect as compared to exposure with Fe and Mn. The 96 hr LC50 value for Ni exposure was 0.321 mg/mL (approximately 30% inhibition), whereas Mn was the second most toxic metal followed by Fe with the 96 hr LC50 values of 0.684 mg/mL and 3.020 mg/mL respectively. This study demonstrated that even though Fe and Mn are essential micronutrients for A. flos-aquae, both show toxic effects at high concentrations. The difference in the toxicity value between Fe and Mn for A. flos-aquae is five times and this indicates that Mn was five times more toxic to A. flos-aquae than Fe suggesting that the Cyanobacteria is more tolerant to Fe when compared with Mn.