Dissolved organic carbon (DOC) and particulate organic carbon (POC) play a fundamental role in biogeochemical cycles of freshwater ecosystems. However, the lack of readily available distributed models for carbon export has limited the effective management of organic carbon fluxes from soils, through river networks and to receiving marine waters. We develop a spatially semi-distributed mass balance modeling approach to estimate organic carbon flux at a sub-basin and basin scales, using commonly available data, to allow stakeholders to explore the impacts of alternative river basin management scenarios and climate change on riverine DOC and POC dynamics. Data requirements, related to hydrological, land-use, soil and precipitation characteristics are easily retrievable from international and national databases, making it appropriate for data-scarce basins. The model is built as an open-source plugin for QGIS and can be easily integrated with other basin scale decision support models on nutrient and sediment export. We tested the model in Piave river basin, in northeast Italy. Results show that the model reproduces spatial and temporal changes in DOC and POC fluxes in relation to changes in precipitation, basin morphology and land use across different sub-basins. For example, the highest DOC export were associated with both urban and forest land use classes and during months of elevated precipitation. We used the model to evaluate alternative land use scenarios and the impact of climate on basin level carbon export to Mediterranean. Display omitted •Riverine DOC and POC dynamics reflect sub-basin land use and climate conditions.•Semi-distributed mass balance models show spatial and temporal changes.•An open source QGIS plug-in allows for scenario analysis of alternative land uses.•Future climate scenarios show major reductions of riverine DOC and POC export.