An apparatus is described for withdrawing filtered permeate from a substrate contained in a reservoir at ambient pressure. The apparatus includes a plurality of membrane assemblies. Each assembly has a plurality of hollow fiber filtering membranes, immersed in the reservoir, at least one permeating header with the membranes sealingly secured therein, and a permeate collector to collect the permeate sealingly connected to the at least one permeating header and in fluid communication with lumens of the membranes. The membranes of each assembly extend generally vertically upwards from a first header during permeation. One or more sources of suction are provided in fluid communication with the lumens of the membranes of each assembly through the permeate collectors and apply sufficient suction to withdraw permeate from the lumens of the membranes. An aeration system for discharging bubbles assists in keeping the membranes clean. In other aspects, a method of removing fouling materials from the surface of a plurality of porous membranes includes providing, from within a membrane module, gas bubbles in a uniform distribution relative to the membranes. The bubbles move past the surfaces of the membranes to dislodge fouling materials from them. The membranes are arranged in close proximity to one another and mounted to prevent excessive movement.