The removal of arsenic and pesticides from natural ground water from the Slavonia region, Croatia, by two commercial nanofiltration membranes (NF270 and NFc) was investigated. The nanofiltration membranes and a comparing reverse osmosis membrane were first examined using sodium dibasic arsenate solution and judged against their performances using sodium chloride and sodium sulfate solutions. The rejections of the sodium dibasic arsenate as well as the arsenate anion from the natural groundwater by the nanofiltration membranes are satisfactory high, and one of the nanofiltration membranes exhibit the superior permeation rate values. The outstanding permeation rate values of these membranes in relation to the reverse osmosis membrane promise a noteworthy decrease of energy consumption and energy costs for the process when using these membranes. The prevailing mechanism of ion retention by the negatively charged nanofiltration membranes is the charge exclusion. The size exclusion mechanism is also important but not sufficient for the uncharged organic molecules rejection. The membrane material and the membrane pore size distribution (PSD) also influence the uncharged organic molecules rejections. The rejections of pesticides are reasonably high, and besides the size effect, the specific physicochemical phenomena should be considered in order to understand their rejection by the nanofiltration membranes.