Due to water shortage problems in arid regions such as Arizona, an increasing number of cities use recycled water as a water resource. Soil aquifer treatment (SAT), one method of reclaiming water to increase long term drinking water supplies, utilizes the infiltration of reclaimed water in the subsurface to remove effluent organic matter. An alternative treatment is the use of membrane technology, nanofiltration (NF) or reverse osmosis (RO), with subsequent deep well injection. In this study an optimized DOC isolation approach has been developed for the bulk water characterization of SAT and membrane treated water. For bulk water characterization it was found that after SAT treatment dissolved organic carbon (DOC) and UVA254 were reduced by more than 80 % and after RO treatment by more than 95 %. SUVA254 was found to be a good indicator of the aromatic hydrophobic character of organic matter and SUVA254 after membrane treatment shows much lower values than after SAT treatment. This indicates a different character after SAT and RO treatment. The isolates showed structural differences in fourier transform-infrared spectroscopy (FT-IR), 13C- nuclear magnetic resonance (NMR) spectroscopy and two-dimensional NMR. Includes 15 references, tables, figures.