Riverine transport of carbon and nitrogen strongly impacts terrestrial and aquatic ecosystem functions but is itself affected by changes in land cover and land use. China’s Nen River basin has experienced widespread conversion from forest to cropland in the past century, making it representative of similar global land use changes. We assessed organic carbon and nitrogen transport in this basin during 2018 and 2019, using water samples collected at one-hour intervals during the twelve flood events in two sub-basins (the Yalu and Yin rivers) dominated by forests and cropland, respectively. We also assessed dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) concentrations from 19 sampling sites distributed throughout the Nen River basin, in combination with hydrological records, to investigate the impacts of land cover on riverine carbon and nitrogen fluxes. The forested Yalu river basin showed significantly higher DOC content and lower TDN content than Yin river basin. Riverine DOC concentrations during non-flood periods in the forested Yalu river basin were significantly higher than in the cultivated Yin river basin, but riverine TDN concentrations were lower. Throughout the Nen River basin and its sub-basins, riverine TDN content was proportional to cropland area. During the twelve flood events, riverine DOC and TDN varied widely over time in the Yin and Yalu river basins, possibly due to dilution effects of water originating from different land covers within the basins. Our results demonstrate that land cover is the principal cause of changes in riverine DOC and TDN content in this region.