Peatland streams have repeatedly been shown to be highly supersaturated in both CO2 and CH4 with respect to the atmosphere, and in combination with dissolved (DOC) and particulate organic carbon (POC) represent a potentially important pathway for catchment greenhouse gas (GHG) and carbon (C) losses. The aim of this study was to create a complete C and GHG (CO2, CH4, N2O) budget for Auchencorth Moss, an ombrotrophic peatland in southern Scotland, by combining flux tower, static chamber and aquatic flux measurements from 2 consecutive years. The sink/source strength of the catchment in terms of both C and GHGs was compared to assess the relative importance of the aquatic pathway. During the study period (2007–2008) the catchment functioned as a net sink for GHGs (352 g CO2-Eq m−2 yr−1) and C (69.5 g C m−2 yr−1). The greatest flux in both the GHG and C budget was net ecosystem exchange (NEE). Terrestrial emissions of CH4 and N2O combined returned only 4% of CO2 equivalents captured by NEE to the atmosphere, whereas evasion of GHGs from the stream surface returned 12%. DOC represented a loss of 24% of NEE C uptake, which if processed and evaded downstream, outside of the catchment, may lead to a significant underestimation of the actual catchment-derived GHG losses. The budgets clearly show the importance of aquatic fluxes at Auchencorth Moss and highlight the need to consider both the C and GHG budgets simultaneously.