A commercial polyamide seawater reverse osmosis membrane (Woongjin Chemical CSM) was surface-modified with fluoro-compounds. The effect of this surface modification on both water and NaCl permeability before and after organic fouling was investigated. The structural and electrical characteristics of the membrane surface were measured using atomic force microscopy and electrokinetic analysis respectively. When modified, the membrane surface showed only slight changes to the surface roughness and surface charges. The modified membrane also showed highly improved fouling resistance during cross-flow filtration of characteristic seawater organic foulants (humic acid and sodium alginate). Contact angle analysis using the Owens-Wendt theory was used to calculate the surface energy of the modified membrane. Lower surface energy of the modified membrane was identified as the key factor in the improved fouling resistance of the membranes.