The potential of nanofiltration for the separation of pharmaceutical and estrogenic compounds from salts in urine was investigated with the aim of producing a micropollutant-free nutrient solution that can be used as a fertilizer. A fresh urine solution and a synthetic solution of similar inorganic composition were tested at different pH values in order to investigate their separation behavior. These solutions were spiked with the micropollutants propranolol, ethinylestradiol, ibuprofen, diclofenac and carbamazepine. Among the membranes tested, NF270 showed the best performance with respect to the retention of micropollutants. The optimum retention of micropollutants was obtained at values of around pH 5. At this point, the retention of all micropollutants in non-hydrolysed urine was above 92%, while the corresponding value for the synthetic urine solution was above 73%. From the results, it can be concluded that the retention mechanism is determined by steric and electrostatic effects as well as by the partitioning of the micropollutants in the membrane. The nutrients urea and ammonia were well permeated, but phosphate and sulfate were almost completely retained. Nanofiltration can consequently be used to produce a permeate which contains most of the nitrogen and a greatly reduced proportion of micropollutants.