Sunlight-induced molecular changes have been observed in two samples of dissolved organic matter (DOM) collected in the Cape Fear River system, North Carolina, USA. The molecular composition of a water sample collected in the Black River (sample B210, salinity 0) and another water sample collected within the Cape Fear River estuary (sample M61, salinity 13.7) were analyzed using an ultrahigh resolution 9.4 Tesla (T) electrospray ionization Fourier transform ion cyclotron resonance mass spectrometer. Additionally, the Ultraviolet/Visible (UV/vis) absorbance as well as the excitation emission matrix (EEM) fluorescence spectra were determined to identify changes in the optical properties associated with photochemical reactions of the chromophoric DOM (CDOM). The molecular formulas forthe Cape Fear River Estuary (M61) sample before the irradiation experiments indicated the presence of highly aromatic compounds which were not present in the unirradiated Black River sample (B210). These aromatic compounds, with oxygen-subtracted double bond equivalents (DBE-O) values greater than nine, are more photoreactive and readily photodegraded relative to saturated compounds. Compounds with DBE-O values below nine are less photoreactive. The UV/vis absorbance and EEM fluorescence results supported this different photodegradation behavior, suggesting that the photoreactivity of CDOM is highly dependent on the molecular composition of the CDOM.