A persistent cell labeling dye and a novel microbial counting method were used to explore the effects of salinity on a microbial population in a reverse osmosis (RO) desalination system, and these clearly distinguished microbial cell multiplication from cell adherence. The results indicated that microbial multiplication is more active at the front of a seawater RO pressure vessel, while adhesion dominates the back of the vessel. A severe reduction in RO permeate flux and total dissolved solid (TDS) rejection were detected at low salinity, attributed to marked cell multiplication and release of extracellular polymeric substances, whilst a relatively stable flux was observed at medium and high salinity. The results from PCR-DGGE revealed the variation in microbial species distribution on the membrane with salinity. The results imply the critical role of membrane modification in biofouling mitigation in the desalination process.