Recirculating aquaculture systems (RAS) normally use nitrifying bacteria to control nitrogen compounds. However, some problems from the nitrification process may arise, creating toxic concentrations for the fish. Nanofiltration (NF) could be the answer for this fluctuation, controlling the quality of water in the required level. In this work, we analyze the capacity of NF 270 membrane to reject nitrite and nitrate ions in two different concentrations and using two different water hardness, based on the concentration detecting in RAS in Chile. In the first test, NF membrane was tested at different transmembrane pressures (TMP) in two types of model solutions, formed by nitrite or nitrate dissolved in deionized water, testing two concentrations, high (H) and low (L), according to the concentration that are dangerous for fish in RAS. In this test, NF 270 membrane rejected approximately 75% of nitrite or nitrate, at the best TMP (19 bar). In the second test, the membrane was tested using nitrite, nitrate, and different qualities of water, based on the water hardness produced by different salts, found in RAS in Chile. This water quality was formulated and classified as soft and hard. There, bivalent cations present in the water are rejected in more than 70% and monovalent cations passed easier through the membrane with a rejection between 50 and 80%, depending on N-molecules concentrations and on the water hardness. We can conclude that this phenomenon is related with the hydrated energy and Donnan exclusion. The rejection of the N-molecules in those conditions depends on the concentration and the hardness of the water. For soft water hardness, the rejection was between 40 and 60% for the N-molecules and for hard water quality, this percentage is in the range of 25–40% at 20 bar of TMP. With these results, a membrane process was proposed to separate the nitrite and nitrate from hard water including different steps that should be tested in a prototype.