A membrane bioreactor system includes one or more biological reactors and one or more membrane tanks with each membrane tan having one or more membrane filters. To control membrane fouling, various process control variables are employed. First, the membrane filters are cleaned by an air scouring process where bubbles are moved upwardly adjacent the membrane filters and clea the same in the process. To control membrane fouling, a process is utilized that dynamically varies the air scouring flow rate (V) as a function of transmembrane pressure (TMP). In addition, the process entails allowing permeation to start and stop which results in a series of cycles where each cycle includes a permeation phase and a relaxation phase.