Assessment of the composition, reactivity, and potential health effects of dissolved organic matter (DOM) is an important issue in the regulation and operation of groundwater recharge projects. The composition of DOM in various natural surface waters and reclaimed waters used to recharge the alluvial aquifers of the lower Santa Ana River Basin in California was derived primarily from terpenoid hydrocarbons and amino sugars. Lesser amounts of aromatic sulfonate and alkylphenol polyethoxylate metabolites of anionic and neutral surfactants were detected in reclaimed water, and these metabolites persisted in waters of the Santa Ana River, the Prado Wetland, and the recharge basins. Only small amounts of humic substances derived from tannins and lignins were deposited during storm flow periods in the Prado Wetland, but these amounts were responsible for significant increases in disinfection by-product formation potential in these waters. Colloids composed of bacterial cell wall fragments showed large percentage increases in all waters during storm flow periods.