An aerator for immersed filtering membranes has an aerator shell with openings for discharging bubbles from its upper surface and a shape capable of temporarily containing a volume of air in fluid communication with the openings. The shell is open to tank water below it and located so that discharged bubbles will rise through an assembly of the filtering membranes. The shell may be wholly or partially made of parts of the assemblies of filtering membranes. A supply of air is provided to the air space in the aerators alternating between a high flow rate and a low flow rate in short cycles of between about 10 seconds and 100 seconds. A filtration system has an inlet for adding substrate and an outlet for retentate are located so as to create a horizontal flow of substrate through the tank. Membrane assemblies are located within the horizontal flow of substrate. Aerators as described above are provided and operated as described above.