Removal of naturally occurring strontium (Sr) from groundwater is vital as excessive exposure may lead to bone growth problems in children. Nanofiltration/reverse osmosis (NF/RO) is commonly used in groundwater treatment due to the high effectiveness and simple maintenance of these pressure driven membrane processes. In this research, a pilot-scale NF/RO system was used to desalinate a natural groundwater sample containing high Sr concentration (10.3 mg/L) and “old” groundwater organic matter (70.9 mg/L) from Esilalei in northern Tanzania to understand the removal of strontium by NF/RO. The impact of applied pressure (10–15 bar) and groundwater pH (3–12) on the membrane performance including permeate flux, strontium and total organic carbon (TOC) flux and removal was investigated. Increasing applied pressure was found to enhance the flux by increasing the driving force and enhance Sr and TOC removal by dilution effect (water flux higher than Sr passage). The alkaline pH caused severe flux decline likely due to membrane fouling and scaling, while it slightly enhanced Sr removal of RO membranes, but weakened the TOC removal. In contrast, acidic and neutral pH of groundwater enhanced TOC removal. ... mehrThese findings suggest that appropriately high applied pressure and acidic pH condition of groundwater are recommended to apply to the NF/RO membrane system in groundwater desalination to achieve better membrane performance.