Desalination is considered to be a major source of usable water in the Middle East, especially the Gulf countries which lack fresh water resources. A key and sometimes the only solution to produce high quality water in these countries is through the use of seawater reverse osmosis (SWRO) desalination technology. Membrane fouling is an economic and operational defect that impacts the performance of SWRO desalination technology. To limit this fouling phenomenon, it is important to implement the appropriate type of intake and pre-treatment system design. In this study, two types of systems were investigated, a vertical well system and a surface-water intake at a 9m depth. The purpose of this investigation is to study the impact of the different intake systems and pre-treatment stages in minimizing the concentrations of algae, bacteria, natural organic matter (NOM) and transparent exopolymer particles (TEP), in the feed water prior to pre-treatment, through the pre-treatment stages, and in the product water and concentrate. Water samples were collected from the surface seawater, the intakes (wells for site A, 9 m depth open ocean intake at site B), after the media filter, after the cartridge filter, and from the permeate and reject streams. The measured parameters included physical parameters, algae, bacteria, total organic carbon (TOC), fractions of dissolved NOM, particulate and colloidal TEP. The results of this study prove that the natural filtration and biological treatment of the seawater which occur in the aquifer matrix are very effective in improving the raw water quality to a significant degree. The results demonstrated that algae and biopolymers were 100% removed, the bacterial concentrations were significantly removed and roughly 50% or greater of TOC concentrations was eliminated by the aquifer matrix at site A. The aquifer feeding the vertical wells reduced TEP concentrations, but to differing degree. There is a slight decrease in the concentrations of, algae, bacteria, TOC, NOM, and TEP in the feed water at 9 m depth compared to the surface seawater at site B. The pre-treatment was of significant effectiveness and the improvements in reducing the membrane fouling potential were quite high and strong at this site. Investigation of the permeate stream showed some breakthrough of bacteria which is of concern because it may indicate a problem within the membrane system (e.g., broken seal and perforation). The aquifer feeding the wells in the subsurface system plays a main role in the improvement of water quality, so the pre-treatment seems less effective in site A plant. This proves that the subsurface intake is better than open ocean intake in terms of providing better raw water quality and ultimately reducing membrane biofouling.