A method for operating a water treatment facility, in particular for sea water desalination, this facility comprising: - at least one membrane unit comprising several pressure tubes for filtration by reverse osmosis, or by nanofiltration, an intake pipe (1, 1a) for water to be treated, at least one outlet pipe for the permeate, and a discharge pipe for the concentrate, - at least one high pressure pump on the intake pipe, - and an energy recovery system including a first inlet of water to be treated, a first pressurised outlet of water to be treated connected, with a recirculation pump, to the intake pipe downstream of the high pressure pump, a second inlet connected to the discharge pipe, and a second outlet connected to a drainage pipe for the concentrated water, - a cleaning solution circuit (16, 17, 18) comprising a cleaning solution supply device (16, 16a), - and a set of valves for controlling the filtration operations and the cleaning operations, the flow rate of cleaning solution passing through said at least one membrane unit having to be at least equal to a prescribed value Q for cleaning said at least one membrane unit, the prescribed value of the flow rate of cleaning solution being of between 6 and 9 m 3 /h per pressure tube, characterised in that cleaning said at least one membrane unit comprises: - injecting the cleaning solution upstream of the high pressure pump, at a flow rate Q1 provided by the cleaning solution supply device and less than 0.5 times the prescribed value Q, - recirculating the cleaning solution provided by recirculating solution exiting through the discharge pipe of the membrane unit and flowing through the energy recovery system by at least the additional flow rate (Q-Q1) of cleaning solution, the high pressure pump being stopped during cleaning. - at least one membrane unit comprising several pressure tubes for filtration by reverse osmosis, or by nanofiltration, an intake pipe (1, 1a) for water to be treated, at least one outlet pipe for the permeate, and a discharge pipe for the concentrate, - at least one high pressure pump on the intake pipe, - and an energy recovery system including a first inlet of water to be treated, a first pressurised outlet of water to be treated connected, with a recirculation pump, to the intake pipe downstream of the high pressure pump, a second inlet connected to the discharge pipe, and a second outlet connected to a drainage pipe for the concentrated water, - a cleaning solution circuit (16, 17, 18) comprising a cleaning solution supply device (16, 16a), - and a set of valves for controlling the filtration operations and the cleaning operations, the flow rate of cleaning solution passing through said at least one membrane unit having to be at least equal to a prescribed value Q for cleaning said at least one membrane unit, the prescribed value of the flow rate of cleaning solution being of between 6 and 9 m 3 /h per pressure tube, characterised in that cleaning said at least one membrane unit comprises: - injecting the cleaning solution upstream of the high pressure pump, at a flow rate Q1 provided by the cleaning solution supply device and less than 0.5 times the prescribed value Q, - recirculating the cleaning solution provided by recirculating solution exiting through the discharge pipe of the membrane unit and flowing through the energy recovery system by at least the additional flow rate (Q-Q1) of cleaning solution, - injecting the cleaning solution upstream of the high pressure pump, at a flow rate Q1 provided by the cleaning solution supply device and less than 0.5 times the prescribed value Q, - recirculating the cleaning solution provided by recirculating solution exiting through the discharge pipe of the membrane unit and flowing through the energy recovery system by at least the additional flow rate (Q-Q1) of cleaning solution, the high pressure pump being stopped during cleaning.