Evaluating the extent of CO₂ emissions from lakes exhibiting diverse trophic levels is essential for advancing our current understanding of the influence of ecological and climatic processes on these ecosystems. This research consisted in measuring CO₂ emission during the day hours from lakes located in the Suwałki Lake District and was carried out in the littoral zone using a closed floating chamber. Based on the trophic indexes, oligotrophic, mesotrophic, eutrophic, and dystrophic lakes were distinguished. The emission from all investigated lakes ranged from −0.354 g (CO₂) per m h⁻¹ to 0.142 g (CO₂) per m h⁻¹. This research confirms that lakes could be absorbers or emitters of CO₂ to the atmosphere. Only the Arkadia reservoir was in a state close to equilibrium in the water–air phase system. Most of the lakes were oversaturated with CO₂ resulting in its release to the atmosphere. Their CO₂ excess is widely attributed to in-lake oxidation of terrestrially organic matter. The humic lake despite lower production at the level of about 80 mgC m⁻² d⁻¹ compared to the other lakes (net production > 100) showed a negative CO₂ gradient in the water-to-air system, which resulted in the absorption of CO₂ from the atmosphere. Both natural and anthropogenic factors are crucial in controlling the rate at which CO₂ is released into the atmosphere. An emphasis should be placed on controlling external loadings of organic matter, where decomposition could release CO₂ to the water column and oversaturation results in higher CO₂ emissions to the atmosphere. Engaging in such research has the potential to aid in the formulation of water conservation management strategies. These investigations can further contribute to the development of lake conservation strategies that specifically address the mitigation of CO₂ emissions from these aquatic ecosystems into the atmosphere.