The invention relates to a process for treating freshwater, sea water, brackish water or water exiting a drinking water treatment plant containing organic matter, with a view to the potabilization thereof, recycling thereof, desalination thereof, or with a view to the purification thereof for an industrial application, said process comprising at least a first step (11) of filtration, by a nanofiltration or reverse osmosis, of a flow coming in from a primary treatment step (10) and a second step (13) of filtration, by nanofiltration or reverse osmosis, of a concentrate coming from said first filtration step (11). According to the invention, such a process comprises a step (12, 12′) of intermediate treatment that includes a biological and / or oxidation treatment and / or a coagulation at low pH of said concentrate coming from said first filtration step (11) and / or of said concentrate coming from said second filtration step (13).