Reverse Osmosis (RO) and Nanofiltration (NF) membranes used for surface and groundwater desalination are susceptible to bio-organic fouling (i.e., proteins, humic acid, fulvic acid), colloidal fouling and mineral salt scaling. Membrane fouling and/or scaling not only results in a decreased membrane permeate flux but also protein adhesion and mineral salt scale formation that may permanently alter the physical features of the surface and lead to irreparable membrane damage. Previous strategies for mitigating membrane fouling/scaling (i.e., polymer surface adsorption and UV, gamma irradiation, and low-pressure plasma graft polymerization) have relied on alteration of the membrane surface chemistry and topography by addition of a permselective polymer thin film that would act both as a separation layer and a physical boundary to prevent adsorption of organic and mineral salt species. In the present study, a novel atmospheric pressure plasma-induced graft polymerization method was developed to enable the generation of a high surface density of active surface sites for subsequent graft polymerization using a suitable monomer. The properties of the grafted polymer on the RO and NF membranes, specifically the surface density, polymer chain length, and monomer chemistry, were evaluated with respect to the membrane performance (i.e., onset of mineral scaling, water permeate flux decline and surface scale coverage) to determine the optimal surface structuring conditions required reduce surface fouling/scaling. Bio-organic fouling studies were conducted in a dilute aqueous feed stream of model proteins. Surface scaling was also evaluated by subjecting the surface structured membranes to a dilute aqueous mineral salt solution with the onset of mineral scaling detected by a novel scale-observation imaging system. The results suggest that surface modification of both RO and NF membranes by plasma-induced graft polymerization can be an effective tool for increasing membrane performance by decreasing the propensity for scaling and fouling.