The value and efficiency of microalgal biofuel production can be improved in an integrated system using waste streams as feed-stock, with fuel-rich biomass and treated wastewater being key end-products. We have evaluated seven native cyanobacterial isolates and one native green alga for their nutrient removal, biomass accumulation and lipid production capacities. All native isolates were successfully grown on synthetic wastewater mimicking secondary treated municipal wastewater (without organic carbon). Complete phosphate removal was achieved by the native green alga, isolated from Tvarminne (SW Finland). Optimisation of the C:N ratio available to this strain was achieved by addition of 3% CO2 and resulted in complete ammonium removal in synthetic wastewater. The native green alga demonstrated similar nutrient removal rates and even stronger growth in screened municipal wastewater, which had double the ammonium concentration of the synthetic media and also contained organic carbon. Sequencing of the genes coding for 18S small rRNA subunit and the ITS1 spacer region of this alga placed it in the Scenedesmaceae family. The lipid content of native isolates was evaluated using BODIPY (505/515) staining combined with high-throughput flow cytometry, where the native green alga demonstrated significantly greater neutral lipid accumulation than the cyanobacteria under the conditions studied. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).