The complex effects of ozonation on the photophysical and size-based properties of dissolved organic matter (DOM) were investigated using two DOM isolates, Suwannee River Fulvic Acid (SRFA) and Pony Lake Fulvic Acid (PLFA). A size exclusion chromatography system paired with absorbance, fluorescence, and total organic carbon detection was used to determine the fluorescence quantum yield (Φf) as a function of the apparent molecular weight (AMW). Size-based fractions of each isolate were collected and irradiated to measure singlet oxygen (1O2) quantum yield (Φ1O2). Φf decreased with ozonation in low AMW fractions, while increasing in high AMW fractions. Φ1O2 increased with ozone dose in low AMW fractions from ∼2 to ∼7% and ∼3 to ∼11% for PLFA and SRFA, respectively, indicating that these are the most photoreactive fractions of DOM. Decreases in Φf and concomitant increases in Φ1O2 in low AMW fractions indicated that chemical transformations occurred, likely including the conversion of phenols to quinones, particularly in SRFA. Results further suggest that the photoactive and fluorescent fractions of DOM are likely independent pools of chromophores from different AMW fractions. In PLFA, a linear response in Φ1O2, specific UV absorbance at wavelength 254 nm (SUVA254), and Φf with ozonation indicated the equal distribution of ozone-reactive moieties.