A process is described for withdrawing filtered permeate from a non-pressurized substrate in a reservoir through an assembly. The assembly has a plurality of hollow fiber filtering membranes disposed generally vertically between two solid bodies, an enclosure sealed to the upper solid body to define a cavity, a permeate port in communication with the cavity and the lumen of each membrane in fluid communication with the port via the cavity. A suction is applied to lumens of the membranes via the permeate port to withdraw permeate. A gas is directed to provide bubbles which contact the membranes. Feed water is added so that the membranes are immersed while applying the suction.