Wastewater treatment plants are not specially designed to remove pharmaceutically active compounds (PhACs), since these substances are toxic and bio-refractory. This paper aims to investigate and optimize the performance of the Trisep TS80 nanofiltration (NF) membrane for the removal of a mixture of two of the most detected PhACs in municipal wastewaters worldwide, sulfamethoxazole and diclofenac. Several NF tests were carried out to study the rejections of these contaminants both spiked in demineralized water, filtrated water taken from Mondego River and secondary effluent coming from a municipal wastewater treatment plant. Among the several studied operating variables, pH was the one that most affected the contaminant rejection and membrane permeability. In the case of synthetic effluent, an applied pressure of 10 bar and pH 7 were determined as the best operating conditions, which allowed almost total chemical oxygen demand retention and a global contaminant rejection of 96.3% to be achieved. The application of different water matrices (river water and secondary municipal effluent) had no relevant impact on process efficiency. Vibrio fischeri luminescence inhibition tests revealed that treatment by nanofiltration reduced acute toxicity of all studied effluents.