Analyses of the changes in concentration of algae, bacteria, transparent exopolymer particles (TEP), and the fractions of natural organic matter (NOM) impacts between surface seawater and the discharges of well intake systems were evaluated at seven different seawater reverse osmosis water (SWRO) treatment plants. In nearly all cases, travel of the raw seawater through the seabed into the aquifer and into the wells removed all of the algae. Bacteria removal was up to 98.5 %, but varied greatly between sites and in different wells at each site. The TEP concentration was significantly lowered compared to the natural seawater. The biopolymer fraction of NOM was significantly lowered at all sites, but the lighter fractions of the NOM were removed at lower percentages. The removal percentage of NOM fractions appears to be based on molecular weight (and size) with the lighter weight fractions removed at lower percentages. A key factor controlling the removal of organic material appears to by the hydraulic retention time which is controlled by the length of the flowpath and the type of aquifer porosity. Specific site geology does not seem to be a significant factor. Vertical well systems showed greater organic materials removal compared to horizontal and tunnel intake systems. Again, this appears to be related to the length of the flowpath and the hydraulic retention time. The horizontal well system at Alicante, Spain showed poor removal of organic matter and breakthrough of algae occurred in the system.