Cyanobacteria are commonly found in a number of temperate and tropical bioregions, and provide important roles in fuelling many nutrient poor freshwater and marine ecosystems. Although cyanobacteria commonly occur in these environments, little is known about the use of cyanobacteria as suitable organisms for toxicity studies. Here, we propose the use of the unicellular cyanobacteria Cyanobium sp., as a potential species for tropical toxicity testing using flow cytometry. Cyanobium sp. was isolated from a composite sample of sea water in Halifax Bay, North Queensland, Australia. After careful isolation, cleaning and purification, Cyanobium sp. was used to determine the toxicity of copper, cobalt, and nickel at pH 8, and ammonia at pH 7 and 8. EC10/50 values were calculated using growth inhibition data determined via flow cytometry, which was found to provide rapid, accurate results, with the ability to define multiple endpoints. Cyanobium sp. was particularly sensitive to copper, cobalt and nickel, however, thrived at elevated concentrations of ammonia, irrespective of pH value. The results indicate that Cyanobium sp. is a useful test organism for tropical marine metal toxicity studies, however, is unsuitable for nutrient studies, particularly ammonia.