​Sete Cidades Lake (São Miguel Island, Portugal) is subdivided into two interconnected branches: the Green Lake and Blue Lake. The lake has an area and maximum depth of 4.39 km² and 29.5 m (Blue Lake), respectively, with evidence of eutrophication, particularly in the northern area of the Green Lake. In this study, we conducted a sampling survey during January 2017 to measure CO₂ fluxes from the lake using a floating accumulation chamber. We also produced two hydrogeochemical profiles for each of the lake’s branches. A total of 1760 CO₂ flux measurements were taken along the lake’s surface. The lake water was relatively cold (14.0 °C on average) and weakly mineralised (average electrical conductivity of 116 μS cm⁻¹) with a neutral pH (7.7 on average). The relative composition of major ions occurred in the following decreasing order: Na⁺ > Mg²⁺ > Ca²⁺ > K⁺ for cations and Cl⁻ > HCO₃⁻ > SO₄²⁻ for anions. The lake water was mainly the Na–Cl type due to sea salt input from seawater spraying. CO₂ fluxes ranged from 0.3 to 17.2 g m⁻² d⁻¹ and from 2.1 to 17.9 g m⁻² d⁻¹ for the Blue and Green Lakes, respectively. Highest CO₂ degassing occurred in areas dominated by macrophytes and algal blooms. The measured values suggest that the CO₂ was predominantly biogenically sourced, which was further supported by the δ¹³C isotopic data. The estimated total CO₂ emissions varied between 5.8 t d⁻¹ (Green Lake; area = 0.81 km²) and 24.9 t d⁻¹ (Blue Lake; area = 3.58 km²). This study further elucidates the lake’s trophic and chemical pollution status and has major implications for lacustrine CO₂ emissions to the atmosphere. Our study also provides a reference for understanding potential future variations in volcanic activity.