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Increasing levels of freshwater contaminants, mainly due to anthropogenic activities, have resulted in a great deal of interest in finding new eco-friendly, cost-effective and efficient methods for remediating polluted waters. The aim of this work was to assess the feasibility of using a green microalga <i>Desmodesmus</i> sp., a cyanobacterium <i>Nostoc</i> sp. and a hemicryptophyte <i>Ampelodesmos mauritanicus</i> to bioremediate a water polluted with an excess of nutrients (nitrogen and phosphorus) and heavy metals (copper and nickel). We immediately determined that <i>Nostoc</i> sp. was sensitive to metal toxicity, and thus <i>Desmodesmus</i> sp. was chosen for sequential tests with <i>A. mauritanicus</i>. First, <i>A. mauritanicus</i> plants were grown in the ‘polluted’ culture medium for seven days and were, then, substituted by <i>Desmodesmus</i> sp. for a further seven days (14 days in total). Heavy metals were shown to negatively affect both the growth rates and nutrient removal capacity. The sequential approach resulted in high metal removal rates in the single metal solutions up to 74% for Cu and 85% for Ni, while, in the bi-metal solutions, the removal rates were lower and showed a bias for Cu uptake. Single species controls showed better outcomes; however, further studies are necessary to investigate the behavior of new species.