A method of reducing biofilm formation or removing biofilm in a membrane filtration system comprising the steps of: a. providing a feed solution to a membrane filtration system, wherein the feed solution comprises encapsulated microbubbles under conditions that allow the encapsulated microbubbles to embed in a biofilm in the membrane filtration system; and b. sonicating the encapsulated microbubbles using ultrasonic waves of a selected frequency and amplitude provided by a first transducer, wherein the frequency and amplitude of the ultrasonic waves disrupt the biofilm but do not cause acoustic cavitation of the encapsulated microbubbles; c. collecting a retentate in a retentate collector comprising the disrupted biofilm and the encapsulated microbubbles; and d. treating the retentate with ultrasonic waves produced using a second transducer configured to provide ultrasonic waves of a selected frequency and amplitude, wherein the ultrasonic waves causes cavitation of the encapsulated microbubbles and sonoluminescence of the retentate, wherein the encapsulated microbubbles comprise a gas core and an encapsulation shell comprising a ligand, wherein the ligand binds one or more extracellular polymeric substances in a biofilm, wherein the membrane is housed in a membrane filtration unit and the first acoustic transducer is a single transducer configured to automatically scan the membrane filtration unit or wherein the first acoustic transducer comprises long hydro-filament transducers embedded in the membrane module, and wherein the second acoustic transducer is a single transducer configured to automatically scan the retentate collector unit or wherein the second acoustic transducer comprises long hydro-filament transducers in the retentate collector unit. a. providing a feed solution to a membrane filtration system, wherein the feed solution comprises encapsulated microbubbles under conditions that allow the encapsulated microbubbles to embed in a biofilm in the membrane filtration system; and b. sonicating the encapsulated microbubbles using ultrasonic waves of a selected frequency and amplitude provided by a first transducer, wherein the frequency and amplitude of the ultrasonic waves disrupt the biofilm but do not cause acoustic cavitation of the encapsulated microbubbles; c. collecting a retentate in a retentate collector comprising the disrupted biofilm and the encapsulated microbubbles; and d. treating the retentate with ultrasonic waves produced using a second transducer configured to provide ultrasonic waves of a selected frequency and amplitude, wherein the ultrasonic waves causes cavitation of the encapsulated microbubbles and sonoluminescence of the retentate, wherein the encapsulated microbubbles comprise a gas core and an encapsulation shell comprising a ligand, wherein the ligand binds one or more extracellular polymeric substances in a biofilm, wherein the membrane is housed in a membrane filtration unit and the first acoustic transducer is a single transducer configured to automatically scan the membrane filtration unit or wherein the first acoustic transducer comprises long hydro-filament transducers embedded in the membrane module, and wherein the second acoustic transducer is a single transducer configured to automatically scan the retentate collector unit or wherein the second acoustic transducer comprises long hydro-filament transducers in the retentate collector unit.