An investigation of a sea water reverse osmosis desalination facility located in western Saudi Arabia has shown that aquifer treatment of the raw sea water provides a high degree of removal of natural organic matter (NOM) that causes membrane biofouling. The aquifer is a carbonate system that has a good hydraulic connection to the sea and 14 wells are used to induce sea water movement 400 to 450 m from the sea to the wells. During aquifer transport virtually all of the algae, over 90% of the bacteria, over 90% of the biopolymer fraction of NOM, and high percentages of the humic substance, building blocks, and some of the low molecular weight fractions of NOM are removed. Between 44 and over 90% of the transparent exopolymer particles (TEP) are removed with a corresponding significant reduction in concentration of the colloidal fraction of TEP. The removal rate for TEP appears to be greater in carbonate aquifers compared to siliciclastic systems. Although the production wells range in age from 4 months to 14 years, no significant difference in the degree of water treatment provided by the aquifer was found.