The presence of algae, bacteria, various fractions of natural organic matter (NOM), and transparent exopolymer particles (TEP) in the raw water, after each pretreatment process and in the permeate and concentrate streams, were measured at two SWRO plants to assess biofouling potential. It was found that the most significant process controlling the concentration of algae, bacteria, and the biopolymer and humic substances was the intake type with the subsurface intake discharge showing significant reductions. The mixed media filtration process was marginally useful in removing some TOC and NOM, but had little effect on TEP removal. Some bacterial regrowth may be occurring in the cartridge filters, but the evidence is inconsistent. Significant quantities of the biopolymer and humic substance concentrations were found to be retained in the membranes, but the concentrations were significantly greater in the facility using an open-ocean intake. Bacteria and TEP were found in the permeate stream, which may document bacterial regrowth and TEP production downstream of the membrane process. Measurements of the organic carbon passage through SWRO facilities can be successfully used to evaluate pretreatment process effectiveness and to make SWRO plant operational improvements.