A membrane filtration system comprising one or more submerged ultrafiltration or microfiltration membrane assemblies at ambient pressure, each membrane assembly positioned 100 240 mm from a nearest wall, baffle, or adjacent membrane assembly and no more than 1 meter above a floor and at least 150 mm below the liquid level. Mixed liquor is discharged underneath each membrane assembly to create a vertical flow velocity in a range of 1 8 mm/second along an entire length of the membrane assembly. In a sequenced batch reactor system, a coarse bubble air diffuser for scouring each membrane assembly is supplied with air only during the backwash cycle of the filtration system and not during the filtration cycle. In a membrane bioreactor system, the biological treatment section is physically separated from the filtration section and fine bubble air diffusion is used in the biological treatment section.