Two nanofiltration membranes, a Dow NF 270 polyamide thin film and a TriSep TS 80 polyamide thin film, were investigated for their retention of ionic species when filtering mine influenced water streams at a range of acidic pH values. The functional iso-electric point of the membranes, characterized by changes in retention over a small pH range, were examined by filtering solutions of sodium sulphate. Both membranes showed changes in retention at pH 3, suggesting a zero net charge on the membranes at this pH. Copper mine drainage and synthetic solutions of mine influenced water were filtered using the same membranes. These solutions were characterized by pH values within 2 and 5, thus crossing the iso-electric point of both membranes. Retention of cations was maximized when the feed solution pH was less than the iso-electric point of the membrane. In these conditions, the membrane has a net positive charge, reducing the transmission rate of cations. From the recoveries of a range of cations, the suitability of nanofiltration was discussed relative to the compliance with mine water discharge criteria and the recovery of valuable commodity metals. The nanofiltration process was demonstrated to offer advantages in metal recovery from mine waste streams, concomitantly enabling discharge criteria for the filtrate disposal to be met.