Rejection characteristics of perchlorate ($ClO_4^-$) were examined for commercially available reverse osmosis (RO) and nanofiltration (NF) membranes. A bench-scale dead-end stirred-cell filtration system was employed to determine the toxic ion rejection and the membrane flux. Model water solutions were used to prepare $ClO_4^-$ solutions (approximately, $1,000{mu}g/L$) in the presence of background salts (NaCl, $Na_2SO_4$, and $CaCl_2$) at various pH values (3.5, 7, and 9.5) and solution ionic strengths (0.001, 0.01, and 0.01 M NaCl) in the presence of natural organic matter (NOM). Rejection by the membranes increased with increasing solution pH owing to increasingly negative membrane charge. In addition, the rejection of the target ion by the membranes increased with increasing solution ionic strength. The rejection of $ClO_4^-$ was consistently higher for the RO membrane than for the NF membrane and $ClO_4^-$ rejection followed the order $CaCl_2$ < NaCl < $Na_2SO_4$ at conditions of constant pH and ionic strength for both the RO and NF membranes. The possible influence of NOM on $ClO_4^-$ rejection by the membranes was also explored.