Aquaculture activities in developing countries have raised deep concern about nutrient pollution, especially excess phosphorus in wastewater, which leads to eutrophication. NF, NF90, NF450 and XLE membranes were studied to forecast the potential of nanofiltration and low pressure reverse osmosis in the removal of phosphorus from aquaculture wastewater. Cross-sectional morphology, water contact angle, water permeability and zeta potential of these membranes were first examined. Membrane with higher porosity and greater hydrophilicity showed better permeability. Membrane samples also commonly exhibited high zeta potential value in the polyphosphate-rich solution. All the selected membranes removed more than 90% of polyphosphate from the concentrated feed (75 mg/L) at 12 bar. The separation performance of XLE membrane was well maintained at 94.6% even at low pressure. At low feed concentration, more than 70.0% of phosphorus rejection was achieved using XLE membrane. The formation of intermolecular bonds between polyphosphate and the acquired membranes probably had improved the removal of polyphosphate at high feed concentration. XLE membrane was further tested and its rejection of polyphosphate reduced with the decline of pH and the addition of ammonium nitrate.