The fouling behavior of nanofiltration (NF) membranes by proteins bovine serum album (BSA), lysozyme (LYS), and humic acids (HA), as well as their mixtures was studied in a cross flow bench-scale cell. The similarities and differences of the effects of pH on single and mixed organic foulant systems were compared by analyzing the size distribution and zeta potential of foulants in the feed, and in conjunction with the characterization of fouled NF membranes, respectively. Results showed that the fouling behaviors of both single and the mixed systems were significantly correlative with solution pH, moreover BSA/LYS combined with HA appeared more aggravated fouling behavior than single foulant within the test pH range. For solution pH, this can affect interactions of foulants-foulants and foulants-membrane by changing zeta potential of them. Also, therefore, zeta potential value could be used to predict the fouling behavior of NF. Considering the experimental results, more severe fouling behavior by not only single (HA, BSA, and LYS), but mixed systems (BSA+HA and LYS+HA) occurred at acidic and neutral solution pH.