The removal of glyphosate and aminomethylphosphonic acid (AMPA) with synthetic water was carried out on a lab-scale nanofiltration unit using two membranes, NFX and NFW. The presence of humic acid and some inorganic matters (CaCl2 and NaCl) was tested in the experiment. The results demonstrate that NFX exhibits better separation performance than NFW. The herbicide filtration is found to have little effect on the permeate flux as compared to transmembrane pressure. Intermediate concentrations of NaCl act positively on foulant separation, and an increment of 3.3-5.4 percentage points in foulant rejection is obtained with the addition of 100 mg/L of NaCl. In Contrast, CaCl2 has negative effect on foulant separation during nanofiltration. Humic acid alone shows little influence on the rejection performance, whereas it is slightly improved in the coexistence of humic acid and CaCl2. The nanofiltration technology proves to be a good approach to treat the problem of pesticide micropollution in a one-step process. This work clearly shows that the composition of the water matrices may influence the efficiency of the nanofiltration process in terms of the separation of the micropollutants.