A membrane system was applied for ultrapure water production from the treatment of saline effluent from the canned food industry. The industrial effluent presented a high saline concentration, including sodium chloride, calcium carbonate, calcium sulfates, and magnesium. The effluent was treated using a system of reverse osmosis (RO) and a post-treatment process consisting of ion exchange resins (IEXRs). The RO was accompanied by the addition of a hexametaphosphate dose (2, 6, and 10 mg/L) as an antiscalant to avoid the RO membrane scaling by minerals. In turn, IEXRs were used for water deionization to produce ultrapure water with a reduced concentration of monovalent ions. The antiscalant dose was 6 mg/L, producing clean water from RO permeates with an efficiency of 65–70%. The brine from RO was projected for its reuse in food industry processes. The clean water quality from RO showed 20% total dissolved solids (TDS) removal (equivalent to salts). The antiscalant inhibited the formation of calcium salt incrustation > 200 mg/L, showing low fouling. In turn, anionic resins removed 99.8% of chloride ions, whereas the monovalent salts were removed by a mix of cationic–anionic resin, producing ultrapure water with electrical conductivity 3.