Four UF membranes (denoted GH, GK, PT and PW with MWCO of 1000, 2000, 5000 and 20,000 Da, respectively) and four NF membranes (denoted DL, CK, DK and HL, with an approximate MWCO of 150–300 Da in all cases) were used for the filtration of an effluent generated in a municipal wastewater plant after a secondary treatment. The influence of the most important operating variables (nature and MWCO of the membranes, transmembrane pressure, tangential velocity, and temperature) on the permeate flux was widely discussed, and the resistances to the permeate flux were determined following the resistances in series model. Rejection coefficients for parameters that measure the global pollutant content of the effluent (chemical oxygen demand, total organic carbon, absorbance at 254 nm, turbidity, total nitrogen and total phosphorus) were also evaluated, and the results revealed that both UF and NF are feasible options for the treatment of this effluent, yielding a permeate stream that can be reused in several applications. Finally, 28 pharmaceutical compounds were initially detected in this effluent, and their respective rejection coefficients were determined, with eliminations higher than 75% in the case of NF with the HL membrane. Therefore, it is concluded that NF is an excellent option for the removal of toxic pharmaceuticals in municipal wastewaters.