Accounting for greenhouse gas (GHG) emissions and removals in managed ecosystems has generally focused on direct land–atmosphere fluxes, but in peatlands a significant proportion of total carbon loss occurs via fluvial transport. This study considers the composition of this ‘waterborne carbon’ flux, its potential contribution to GHG emissions, and the extent to which it may change in response to land-management. The work describes, and builds on, a methodology to account for major components of these emissions developed for the 2013 Wetland Supplement of the Intergovernmental Panel on Climate Change. We identify two major components of GHG emissions from waterbodies draining organic soil: i) ‘on site’ emissions of methane (and to a lesser extent CO2) from drainage ditches located within the peatland; and ii) ‘off site’ emissions of CO2 resulting from downstream oxidation of dissolved and particulate organic carbon (DOC and POC) within the aquatic system. Methane emissions from ditches were found to be large in many cases (mean 60 g CH4 m−2 year−1 based on all reported values), countering the view that methane emissions cease following wetland drainage. Emissions were greatest from ditches in intensive agricultural peatlands, but data were sparse and showed high variability. For DOC, the magnitude of the natural flux varied strongly with latitude, from 5 g C m−2 year−1 in northern boreal peatlands to 60 g C m−2 year−1 in tropical peatlands. Available data suggest that DOC fluxes increase by around 60 % following drainage, and that this increase may be reversed in the longer-term through re-wetting, although variability between studies was high, especially in relation to re-wetting response. Evidence regarding the fate of DOC is complex and inconclusive, but overall suggests that the majority of DOC exported from peatlands is converted to CO2 through photo- and/or bio-degradation in rivers, standing waters and oceans. The contribution of POC export to GHG emissions is even more uncertain, but we estimate that over half of exported POC may eventually be converted to CO2. Although POC fluxes are normally small, they can become very large when bare peat surfaces are exposed to fluvial erosion. Overall, we estimate that waterborne carbon emissions may contribute about 1–4 t CO2-eq ha−1 year−1 of additional GHG emissions from drained peatlands. For a number of worked examples this represented around 15–50 % of total GHG emissions.