A reverse osmosis system and method includes a pump pressurizing a feed stream, a first and second membrane array that generates permeate and brine streams. A first energy recovery device uses first energy from the second brine stream to pressurize the first brine stream. A first and second auxiliary and bypass valves are associated with the first and second energy recovery device. A second energy recovery device uses second energy from the second brine stream to increase a second pressure of the feed stream. A first flowmeter generates a first flow signal for the first permeate stream. A second flowmeter generates a second flow signal for of the second permeate stream. A third flowmeter generates a third flow signal for the second brine stream. A motor drives the first energy recovery device. A controller controls the in response to the flow signals.