Despite extensive studies on the relationship between membrane surface properties and fouling, the roles of specific surface functional groups in RO membrane fouling under different solution conditions are still poorly understood. This research aims to elucidate how specific surface functional groups affect RO membrane fouling by alginate in solution conditions relevant to seawater desalination. Common RO membrane surface functionalities are represented by self-assembled mono-layers with –COOH, –NH2, –CONH2 and –OH ending groups. Alginate adsorption and removal was studied under relevant solution conditions using quartz crystal microbalance with dissipation monitoring (QCM-D). The results show that ionic composition has great impacts on alginate–alginate interaction, which is more important than membrane surface chemistry in determining alginate adsorption equilibrium at the high ionic strength of seawater. The initial adsorption rate is highly sensitive to surface chemistry. The –NH2 group has strong affinity for alginate, yet the –COOH group exhibits the highest adsorption rate in simulated seawater. The reversibility of the adsorbed layer was influenced by both alginate–surface interaction and the structure of the layer. The large alginate aggregates formed in the presence of Ca2+ result in loosely packed and less viscous adsorbed layer on the surface, which is easier to remove by surfactant cleaning.