Hydrophobic acid (HPO-A) and transphilic acid (TPI-A) fractions of dissolved organic matter (DOM) were isolated from a domestic secondary wastewater effluent that was polished via soil aquifer treatment (SAT). Fractions were isolated using XAD resin adsorption chromatography from samples obtained along the vadose zone flowpath at a full-scale basin recharge facility in Tucson, Arizona. Changes in isolate character during SAT were established via biodegradability (batch test), specific ultraviolet light absorbance (SUVA), trihalomethane formation potential (THMFP), and Ames mutagenicity assays. The dissolved organic carbon (DOC) concentration decreased by >90% during SAT. A significant fraction (up to 20%) of isolated post-SAT HPO-A was biodegradable. The (apparent) refractory nature of DOM that survives SAT may be a consequence of low DOC concentration in groundwater as well as the nature of the compounds themselves. Specific THMFP (µg THM per mg DOC) of HPO-A and TPI-A varied little as a consequence of SAT, averaging 52 and 49 µg THM per mg DOC, respectively. The nonbiodegradable fractions of HPO-A and TPI-A exhibited higher reactivities: 89 and 95 µg THM per mg DOC, respectively. Genotoxicity of HPO-A (on a per mass basis) increased after SAT, suggesting that responsible compounds are removed less efficiently than bulk organics during vadose zone transport.