Water desalination has the potential to alleviate a significant part of the world’s thirst, with a majority of desalinated water capacity coming from seawater reverse osmosis (SWRO). However, SWRO membrane systems suffer from the loss of performance due to biofouling leading to economic costs. There is no control or preventive strategy for SWRO biofouling and current industry practices recommend chemical treatments to restore membrane performance. Chemical cleaning results in high economic costs due to chemical acquisition, storage, transportation, long plant downtimes and ultimately shorter membrane lifetime and early replacement; in addition to the environmental impact associated with disposing of chemicals. Therefore, there is a need for novel effective green cleaning strategies for SWRO to meet the increasing demand for desalinated water while taking care of the environment. Micronanobubbles (MNBs) consist of small gas cavities formed in aqueous solutions. This study evaluates the efficiency of both air-filled micronanobubbles (AMNBs) and CO2 nucleated MNBs as: i) curative cleaning-in-place (CIP) treatments and ii) preventive daily treatments for biofouling over long-term studies. Experiments were performed using the membrane fouling simulator (MFS) under conditions that are representative of SWRO membrane systems. Pressure drop was implemented as the main biofilm growth monitoring parameter as used by standard industry practices. Curative studies showed that both MNBs CIP treatments had high cleaning efficiencies of 49-56% pressure drop recovery. MNBs pressure drop recovery values were close to the conventional chemical cleaning (NaOH/HCl) at 51% and were significantly higher than the hydraulic flush (HF) physical cleaning control at 24%. The pressure drop recovery results were supported by the optical coherence tomography (OCT) images before and after CIP and biomass autopsy results. Similarly, preventive MNBs daily treatments showed a significant delay in the system’s performance decline. This delay was 5.1 days for the CO2 MNBs experiments, 4 days for the AMNBs, and only 0.6 days for the hydraulic flushing treatments compared to the control. Compared to the control the duration of the operation was doubled in time before the cleaning criteria was met. OCT images confirmed biofilm growth delay with lower biomass occurrence.