The application of low-pressure nanofiltration (NF) was investigated for three different applications: water reuse from acid mine drainage (AMD), surface water containing natural organic matter (NOM) and agricultural reuse of microfiltered biologically treated sewage effluent (MF-BTSE). AMD contains many valuable rare earth elements (REEs) and copper (Cu) that can be recovered with fresh water. The NF90 membrane was investigated for recovery of fresh water from synthetic AMD. A steady permeate flux of 15.5 ± 0.2 L/m2h was achieved for pretreated AMD with over 98% solute rejection. NF90 achieved a high dissolved organic carbon (DOC) rejection of 95% from surface water containing NOM where 80% of the organic fraction was hydrophilic, mainly humics. The NF process maintained a high permeate flux of 52 LMH at 4 bars. The MF-BTSE was treated by NTR-729HF for agricultural reuse. NTR-729HF membranes were capable of rejecting DOC and inorganics such as sulfates and divalent ions (SO42−, Ca2+ and Mg2+) from MF-BTSE, with less than 20% rejection of monovalent (Na+ and Cl−) ions. The sodium adsorption ratio (SAR) was significantly reduced from 39 to 14 after treatment through NTR-729HF at 4 bar. The resulting water was found to be suitable to irrigate salt-sensitive crops.