Permafrost-affected soils contain large quantities of soil organic carbon (SOC). Changes in the SOC pool of a particular ecosystem can be related to its net ecosystem carbon balance (NECB) in which the balance of carbon (C) influxes and effluxes is expressed. For polygonal tundra landscapes, accounts of ecosystem carbon balances in the literature are often solely based on estimates of vertical carbon fluxes. To fill this gap, we present data regarding the lateral export rates of dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) from a polygonal tundra site in the north Siberian Lena River delta, Russia. We use water discharge observations in combination with concentration measurements of waterborne carbon to derive the lateral carbon fluxes from one growing season (2 June–8 September 2014 for DOC, 8 June–8 September 2014 for DIC). To put the lateral C fluxes into context, we furthermore present the surface–atmosphere eddy covariance fluxes of carbon dioxide (CO2) and methane (CH4) from this study site. The results show cumulative lateral DIC and DOC fluxes of 0.31–0.38 and 0.06–0.08 g m−2, respectively, during the 93 d observation period (8 June–8 September 2014). Vertical turbulent fluxes of CO2-C and CH4-C accumulated to −19.0 ± 1.2 and 1.0 ± 0.02 g m−2 in the same period. Thus, the lateral C export represented about 2 % of the net ecosystem exchange of (NEE) CO2. However, the relationship between lateral and surface–atmosphere fluxes changed over the observation period. At the beginning of the growing season (early June), the lateral C flux outpaced the surface-directed net vertical turbulent CO2 flux, causing the polygonal tundra landscape to be a net carbon source during this time of the year. Later in the growing season, the vertical turbulent CO2 flux dominated the NECB.