An integrated system was implemented for water phytoremediation and biofuel production through sequential cultivation of filamentous algae followed by cultivation of lipid-producing microalgae Chlorella sorokiniana. Natural poly-culture of filamentous algae was grown in agricultural stormwater using the Algal Turf Scrubber (R), harvested and subjected for lipid extraction and/or methane production using anaerobic digestion (AD). While filamentous algae lipid content was too low for feasible biodiesel production (<2%), both whole biomass and lipid-extracted algal residues (LEA) yielded similar to 0.2 L methane per gVS at loading rates up to 5 g VS/L-day. Importantly, essential macro-nutrients and trace elements captured from stormwater were released into the AD effluent as soluble nutrients and were successfully tested as fertilizer replacement for cultivation of lipid-accumulating C. sorokiniana in a subsequent stage. Accordingly, filamentous algae poly-culture was exploited for waste nutrient capturing and biofuel feedstock generation. These nutrients were recovered and reused as a concentrated supplement for potentially high-value microalgae. Published by Elsevier Ltd.