We use a unique data set of 8 years of continuous carbon dioxide (CO₂) and methane (CH₄) surface water measurements from a commercial ferry to study upwelling in the Baltic Sea. Its seasonality and regional and interannual variability are examined. Strong upwelling events drastically increase local surface CO₂ and CH₄ levels and are mostly detected in late summer after long periods of impaired mixing. We introduce an extrapolation method to estimate regional upwelling-induced trace gas fluxes.