Riverine export of terrestrial organic carbon (TOC) plays an important role in the global C cycle through influences on coastal productivity, sedimentary preservation, and CO2 efflux. In order to examine the influence of hydrologic variability and upland processes on TOC export from a midwestern agricultural watershed, we applied lignin phenol and stable carbon isotope analyses to assess quantity, source, and relative degradation state of TOC in soils, sediments, and size-fractioned aquatic OC from stream water. Flood conditions exported 90 times more dissolved organic carbon (DOC) than baseflow owing to increases in both discharge and concentration, indicating mobilization of additional DOC pools. These observations are supported by increased TOC contributions to aquatic OC during flooding. Furthermore, stable carbon isotope values show that OC exported during flooding is enriched in C4-derived C by up to 38% (for high molecular weight DOC) with respect to baseflow, indicating different TOC sources are mobilized dependant on hydrologic conditions. Lignin phenols isolated from the colloid size fraction show progressive increases in the ratio of carboxylic acid to aldehyde functional groups (a measure of relative degradation state) with distance downstream suggesting selective partitioning to mineral surfaces and/or degradation to this size fraction. This study shows that TOC quantity, source, and relative degradation state can change dependant on hydrologic conditions and in-stream transport in a small agricultural watershed. Moreover, these results are important in showing variability in TOC source and chemistry exported from headwater systems that might otherwise not be detected in studies of larger rivers.