This study demonstrates the removal efficiency and the permeate flux behavior during cross-flow nanofiltration (NF) of aqueous solutions of five pharmaceutically active compounds (PhACs). Cephalexin, tetracycline, acetaminophen, indomethacin and amoxicillin were used as models of PhACs, and alginate was selected as model of natural organic matter (NOM). Two commercial composite NF membranes (SR2 and SR3) with different characteristics were used. The highest rejection was observed for tetracycline, i.e., 75-95% for membrane SR 2 and 95-100% for membrane SR 3, while the rejection was least for acetaminophen (32-36% for SR2 and 52-59% for SR3). As the pH of acetaminophen solution was increased (from 6 to 9) the rejection would increase. Changes of ionic content (from 10 to 20mM) lead to increase (from 89 to 93% for SR 3) or decrease (from 100 to 91% for SR2) of cephalexin rejection depending on the membrane used. The permeate flux would decrease with decreasing the pH solution and increasing ionic strength. The addition of alginate in the feed stream decreased the permeate flux, with lower reduction for SR3, and increased the PhAC rejection except for acetaminophen and amoxicillin. Both size and Donnan exclusions seemed to occur, and the effect of Donnan exclusion was more pronounced for the NF membrane having larger effective pore size (SR2).