Lakes and streams in mountain regions are important contributors to carbon (C) fluxes. However, detailed carbon balances of the stream‐lake continuum are rare. Combining eddy covariance (EC) measurements of lake‐atmosphere net ecosystem CO2 exchange with measurements of fluvial C fluxes (dissolved organic C, DOC; particulate organic C, POC; dissolved inorganic C, DIC), and in‐lake sedimentation, we here present a detailed annual C balance of an oligotrophic clearwater lake in the eastern European Alps. The C flux into the lake was 1522 Mg C year−1 by DIC (93%), DOC (6%), and POC (0.7%). The largest C losses were fluvial exports (1595 Mg C year−1) of DIC (93%), DOC (6%), and POC (0.8%), while sedimentation accounted for 7.3 Mg C year−1. The residual of all fluvial and sedimentation fluxes revealed the lake as a net sink of atmospheric CO2 of 77 Mg C year−1. The EC measurement confirmed a small positive or negative contribution of atmospheric exchange to the lake C balance. In‐lake transfer among C pools was only significant for the flux from DIC to POC (8.4 Mg C year−1), which, following our model, is the transfer through primary production in summer. Fluvial DOC and DIC fluxes were controlled by discharge; POC retention and sedimentation depended on the meteorological season and in‐lake residence time. Following our findings, we conclude that hydrology acted as the most important control for the C balance of this clearwater mountain lake by controlling inflow, outflow, and sedimentation fluxes.