Dissolved organic matter (DOM) transport during storms is studied because it is important in the annual watershed export budget for dissolved organic carbon (DOC). We sampled stream water from two watersheds (upland and wetland-dominated) and three subcatchments (bog, forested wetland, and mineral forest) located within the wetland-dominated watershed during a fall and summer storm to investigate changes in the magnitude and chemical quality of DOM during stormflows. Stormflow export of DOC ranged from 2.3 kg C ha−1 in the upland watershed to 13.9 kg C ha−1 in the bog subcatchment. Biodegradable DOC (BDOC) export for these same storms ranged from 0.6 kg C ha−1 in the upland watershed to 4.2 kg C ha−1 in the bog subcatchment. The percent BDOC decreased during both storms in the upland watershed, while percent BDOC increased in the three wetland streams. Parallel factor analysis (PARAFAC) modeling of fluorescence excitation-emission matrices further showed that as stream water DOM concentrations increased during stormflows in the upland watershed, the contribution of protein-like fluorescence decreased and humic-like fluorescence increased. However, the contribution of protein-like fluorescence increased and humic-like fluorescence decreased slightly in the three wetland streams. These results indicate that shifts in the biodegradability and chemical quality of DOM are different for upland and wetland watersheds. Taken together, our findings suggest stormflows are responsible for substantial export of BDOC from coastal temperate watersheds. Moreover, we found that PARAFAC modeling of fluorescent DOM is an effective tool for elucidating shifts in the quality of stream water DOM during storms.