The present work investigates nanofiltration (NF) and ultrafiltration (UF) for the removal of three widely used pharmaceutically active compounds (PhACs), namely atenolol, sulfamethoxazole, and rosuvastatin. Four membranes, two polyamide NF membranes (NF90 and NF270) and two polyethersulfone UF membranes (XT and ST), were evaluated in terms of productivity (permeate flux) and selectivity (rejection of PhACs) at pressures from 2 to 8 bar. Although the UF membranes have a much higher molecular weight cut-off (1000 and 10,000 Da), when compared to the molecular weight of the PhACs (253–482 Da), moderate rejections were observed. For UF, rejections were dependent on the molecular weight and charge of the PhACs, membrane molecular weight cut-off (MWCO), and operating pressure, demonstrating that electrostatic interactions play an important role in the removal of PhACs, especially at low operating pressures. On the other hand, both NF membranes displayed high rejections for all PhACs studied (75–98%). Hence, considering the optimal operating conditions, the NF270 membrane (MWCO = 400 Da) presented the best performance, achieving permeate fluxes of about 100 kg h⁻¹ m⁻² and rejections above 80% at a pressure of 8 bar, that is, a productivity of about twice that of the NF90 membrane (MWCO = 200 Da). Therefore, NF270 was the most suitable membrane for this application, although the tight UF membranes under low operating pressures displayed satisfactory results.