An investigation of three seawater reverse osmosis facilities located along the shoreline of the Red Sea of Saudi Arabia that use well intake systems showed that the pumping-induced flow of raw seawater through a coastal aquifer significantly improves feed water quality. A comparison between the surface seawater and the discharge from the wells shows that turbidity, algae, bacteria, total organic carbon, most fractions of natural organic matter (NOM), and particulate and colloidal transparent exopolymer particles (TEP) have significant reductions in concentration. Nearly all of the algae, up to 99% of the bacteria, between 84 and 100% of the biopolymer fraction of NOM, and a high percentage of the TEP were removed during transport. The data suggest that the flowpath length and hydraulic retention time in the aquifer play the most important roles in removal of the organic matter. Since the collective concentrations of bacteria, biopolymers, and TEP in the intake seawater play important roles in the biofouling of SWRO membranes, the observed reductions suggest that the desalination facilities that use well intakes systems will have a potentially lower fouling rate compared to open-ocean intake systems. Furthermore, well intake system intakes also reduce the need for chemical usage during complex pretreatment systems required for operation of SWRO facilities using open-ocean intakes and reduce environmental impacts.