Natural soil pipes, which have been widely reported in peatlands, have been shown to contribute significantly to total stream flow. Here, using measurements from eight pipe outlets, we consider the role of natural pipes in the transport of fluvial carbon within a 17.4-ha blanket-peat-covered catchment. Concentrations of dissolved and particulate organic carbon (DOC and POC) from pipe waters varied greatly between pipes and over time, ranging between 5.3 and 180.6 mg L−1 for DOC and 0.08 and 220 mg L−1 for POC. Pipes were important pathways for peatland fluvial carbon export, with fluxes varying between 0.6 and 67.8 kg yr−1 (DOC) and 0.1 and 14.4 kg yr−1 (POC) for individual pipes. Pipe DOC flux was equivalent to 20% of the annual DOC flux from the stream outlet while the POC flux from pipes was equivalent to 56% of the annual stream POC flux. The proportion of different forms of aquatic carbon to total aquatic carbon flux varied between pipes, with DOC ranging between 80.0% and 91.2%, POC from 3.6% to 17.1%, dissolved CO2-C from 2.4% to 11.1% and dissolved CH4-C from 0.004% to 1.3%. The total flux of dissolved CO2-C and CH4-C scaled up to all pipe outlets in the study catchment was estimated to be 89.4 and 3.6 kg yr−1 respectively. Overall, pipe outlets produced discharge equivalent to 14% of the discharge in the stream but delivered an amount of aquatic carbon equivalent to 22% of the aquatic carbon flux at the catchment outlet. Pipe densities in blanket peatlands are known to increase when peat is affected by drainage or drying. Hence, environmental change in many peatlands may lead to an increase in aquatic carbon fluxes from natural pipes, thereby influencing the peatland carbon balance and downstream ecological processes.