We used data collected from 1989 to 2009 from 151 shallow (mean depth < 3 m) temperate lakes in Denmark to explore the influence of lake trophic status, surface area and catchment size on the seasonal dynamics of the air–water flux of CO2. Monthly CO2 fluxes were derived from measurements of acid neutralizing capacity (ANC), pH, ionic strength, temperature, and wind speed. CO2 fluxes exhibited large seasonal variability, in particular in oligo-mesotrophic lakes. Most of the lakes emitted CO2 during winter (median rates ranging 300–1,900 mg C m−2 day−1), and less CO2 during summer or, in the case of some of the highly eutrophic lakes, retained CO2 during summer. We found that seasonal CO2 fluxes were strongly negatively correlated with pH (r = −0.65, P < 0.01), which in turn was correlated with chlorophyll a concentrations (r = 0.48, P < 0.01). Our analysis suggests that lake trophic status (a proxy for pelagic production) interacts with the lake ANC to drive the seasonal dynamics of CO2 fluxes, largely by changing pH and thereby the equilibrium of the free CO2 and bicarbonate relation. Long-term observations from four lakes, which have all undergone a period of oligotrophication during the past two decades, provide further evidence that CO2 efflux generally increases as trophic status decreases, as a consequence of decreased pH. Across these four lakes, the annual average CO2 emission has increased by 32% during the past two decades, thus, demonstrating the strong link between lake trophic status and CO2 flux.