Dissolved organic carbon (DOC) constitutes a small yet important part of a watershed’s carbon budget because it is mobile and biologically active. Agricultural conservation practices such as native perennial vegetation (NPV) strips will influence carbon cycling of an upland agroecosystem, and could affect how much DOC enters streams in runoff, potentially affecting aquatic ecosystems. In a study conducted in Iowa (USA), four treatments with strips of NPV varying in slope position and proportion of area were randomly assigned among 12 small agricultural watersheds in a balanced incomplete block design. Runoff samples from 2008 to 2010 were analyzed for DOC and correlated with flow data to determine flow weighted DOC concentrations and loads. Data were analyzed for the entire 3 years, annually, seasonally, monthly, by flow event size and for one extreme storm event. Overall we found few differences in DOC concentration with the exception that concentrations were greater in the 10 % NPV at the footslope watersheds than the 20 % NPV in contours watersheds over the 3 years, and the 100 % agricultural treatment had higher DOC concentrations than all NPV treatments during the one extreme event. Because the NPV treatments reduced runoff, DOC export tended to be highest in the 100 % agricultural watersheds over the 3 years and during high flows. We also compared two watersheds that were restored to 100 % NPV and found decreases in DOC concentrations and loads indicating that complete conversion to prairie leads to less watershed DOC export. Regression results also support the contention that increases in the percentage of NPV in the watershed decreases watershed export of DOC. Further analysis indicated that DOC concentrations were diluted as flow event size increased, independent of any treatment effects. It appears groundwater sources become an important component to flow as flow event size increases in these watersheds.