The fertilizer industry generates effluents with large amounts of fluoride and phosphate. The objective of this study was to investigate the removal efficiency of reverse osmosis (RU) and nanofiltration (NF) membranes to reduce fluoride and phosphate load to less than 8 mg L-1 and 2 mg L-1, respectively. Separation membranes were characterized indirectly by solute transport method determining pore size and pore size distribution in the selective membranes' layer. The characterization showed unimodal pore size distributions (PSDs) for RO membranes (LFC, ULP and XLE) and tight NF membrane (NF90) with most pores of 0.70 nm and 0.82 nm, respectively. Completely different PSD had the loose NF membrane, HL, which was bimodal with two clearly separated peaks. The presented laboratory study indicated that the rejections of fluoride with RO membranes were higher than 80% (model waters) and higher than 96% (real wastewater), and with NF membranes higher than 40%. Rejections of phosphates were higher: >95% (model waters) and >97% (real wastewater). RO/NF emerged as the promising processes to effectively remove fluoride and phosphate from fertilizer wastewater and meet all MCLs according to the Croatian law. (C) 2010 Elsevier B.V. All rights reserved.