Land-based aquaculture provides dietary protein to the world's population in a sustainable way, but issues related to release of nitrogen rich wastewater limits its expansion. Sedimentation of naturally occurring microalgae that assimilate excess nitrogen, is slow and land intensive. Electro-flocculation, used in wastewater treatment processes, is a potential alternative for aquaculture. Trials of different electro-flocculation configurations applied to three prawn farm pondwater samples containing varying microalgal assemblages are reported. In 64 % of trials, electro-flocculation reduced total nitrogen (TN) and dissolved inorganic nitrogen (DIN) loads within regulatory limits. TN was reduced up to 83.2 % (10.93 to 1.83 mg.L−1) within 20 mins in stationary water, and DIN to 90.6 % (3.19 to 0.30 mg.L−1) in 102 mins trials in flowing water. Bellerochea and Gloeocapsa spp. were dominant in wastewater. The role of microalgal community composition on flocculation is discussed, including evidence Bellerochea promotes flocculation. This study confirmed electro-flocculation quickly reduces TN and DIN.