Abstract Ammonium is known to be one of the most significant pollutants in water bodies. The presence of ammonium in water is mainly originated from agricultural activities, domestic sewage and industrial effluent. This study evaluates the performance of two commercial thin film composite (TFC) membranes, i.e., NF270 and XLE from FilmTec™ for ammonium removal using synthetic wastewater and domestic sewage. The filtration experiment was conducted at different feed ammonium concentrations, humic acid concentrations, pHs and pressure. Results showed that the membrane rejection against ammonium increased dramatically with increasing ammonium concentration. However, the membrane flux was slightly compromised at higher ammonium concentration. With respect to pH, highest ammonium removal rate was able to be achieved at an optimum pH of 10. Besides, the permeation flux increased gradually with increasing feed pressure. From the results, the XLE membrane outperformed the NF270 membrane in terms of ammonium rejection. The retentate of XLE membrane filtration process was found to be useful as liquid fertiliser for plant growth. The results indicated that the TFC membrane process is not only able to produce permeate with an ammonium concentration below the acceptable limit of 10 mg/L but also able to produce retentate with enriched ammonium for plant growth.