Direct land-to-atmosphere carbon exchange has been the primary focus in previous studies of peatland disturbance and subsequent restoration. However, loss of carbon via the fluvial pathway is a significant term in peatland carbon budgets and requires consideration to assess the overall impact of restoration measures. This study aimed to determine the effect of peatland land management regime on aquatic carbon concentrations and fluxes in an area within the UK's largest tract of blanket bog, the Flow Country of northern Scotland. Three sub-catchments were selected to represent peatland land management types: non-drained, drained, and restoration (achieved through drain blocking and tree removal). Water samples were collected on a fortnightly basis from September 2008 to August 2010 at six sampling sites, one located upstream and one downstream within each sub-catchment. Concentrations of dissolved organic carbon (DOC) were significantly lower for the upstream non-drained sub-catchment compared to the drained sub-catchments, and there was considerable variation in the speciation of aquatic carbon (DOC, particulate organic carbon (POC), CO2, and CH4) across the monitoring sites, with dissolved gas concentrations inversely correlated with catchment area and thereby contributing considerably more to total aquatic carbon in the smaller headwater catchments. Significantly higher POC concentrations were observed in the restored sub-catchment most affected by tree removal. Aquatic carbon fluxes were highest from the drained catchments and lowest from the non-drained catchments at 23.5 and 7.9 g C m−2 yr−1, respectively, with variability between the upstream and downstream sites within each catchment being very low. It is clear from both the aquatic carbon concentration and flux data that drainage has had a profound impact on the hydrological and biogeochemical functioning of the peatland. In the restoration catchment, carbon export varied considerably, from 21.1 g C m−2 yr−1 at the upper site to 10.0 g C m−2 yr−1 at the lower site, largely due to differences in runoff generation. As a result of this hydrological variability, it is difficult to make definitive conclusions about the impact of restoration on carbon fluxes, and further monitoring is needed to corroborate the longer-term effects.