Currently, water desalination is an essential solution for the high demand for water worldwide. A sea water reverse osmosis (SWRO) facility fulfills the need for pure water. Conventionally, these plants use open-ocean water that is rich with natural organic matter (NOM) and transparent exo-polymers (TEP). Marine flora increases the demand for fouling the membrane in the SWRO facility that raises the pressure and results in the halting of the station. Therefore, water samples were collected from SWRO stages during high-pressure problems to probe the factors that play a key role in membrane biofouling. NOM and TEP particles physically disappeared after the dual-media filter (DMF). However, turbidity significantly increased after the DMF stage, which is indicative of the fragmentation of NOM and TEP particles. Chlorophyll and phycoerythrin disappeared after the DMF stage but were observed in the reject stage (brine). Therefore, NOM and TEP are playing a role indirectly in membrane biofouling. Fifteen potential species of heterotrophic prokaryotes are identified and recorded in all stages of the SWRO. The characteristics of these species imply that they form a cooperative consortium that potentially creates the biofilm in the RO membrane. Therefore, SWRO facilities that use open-ocean water must develop highly sophisticated pretreatment technology to eliminate the seeds of the biofilm that fouls RO membranes.