Fluvial dissolved and particulate organic carbon concentrations, [DOC] and [POC], were measured weekly in two contrasting catchments in east Iceland in June and July 2016. Sampling was carried out at ten sites in each catchment, including the outlets. [DOC] ranged from 2.1 to 6.6 mg L−1, and [POC] from 0.4 to 3.1 mg L−1. Mean TOC fluxes over the sampling period amounted to 0.46 μg m−2 s−1 from the West catchment and 0.42 μg m−2 s−1 from the East catchment. Concentration and flux data were used to analyse the relationship between organic carbon budgets and different land cover: heathland, wetland, sparse vegetation and dense Nootka lupin (Lupinus nootkatensis). Wetland area, associated with C-rich Histic Andosols, was found to have a significant positive influence on in-stream organic carbon concentrations and fluxes, and the opposite was found with sparsely vegetated areas, likely due to limited soil development. Areas with dense lupin cover were associated with relatively-low organic carbon fluxes in the East catchment, possibly because lupin stabilises its substrate, reducing mobilisation of DOC and POC. In the West catchment this influence was not clear, but this is likely due to the co-location of wetland, causing increased C exports.