Nanofiltration (NF) of ammoniacal wastewater containing phenol and cyanide has been investigated for effective separation of these hazardous pollutants and for the subsequent downstream chemical treatment resulting in valuable by-product generation. Four different types of composite polyamide commercial NF membranes (Sepro, USA) were tested under different operating conditions including transmembrane pressure and recovery rate (RR). At a transmembrane pressure of 15 bar, the achieved rejection of cyanide and phenol were 95% and 93%, respectively (concentrated stream) when the permeate contained 85% of ammonium-N. A high flux of 120 L m−2 h−1 was achieved during NF at a concentrated mode, with a volumetric cross-flow rate of 800 L h−1 at a pH of 10.0. The RR was 60% for the NF1 membrane. Fenton's reagents (7.0 and 3.75 g L−1 H2O2 and FeSO4·7H2O, respectively) were used to degrade more than 99% of pollutants present in the concentrated stream. In the permeate side, 97% of was precipitated out as struvite by using Mg2+:NH4:PO4+ in 1:1:1 molar ratio at pH 9.0.