​Chemical and isotopic vertical profiles from the volcanic lakes of Sete Cidades, Santiago, Fogo, Congro and Furnas (Island of São Miguel, Azores Archipelago, Portugal) were studied to investigate the biogeochemical processes acting at different depths, with a focus on the CO₂ and CH₄ dynamics. These lakes are fed by meteoric water affected by seawater spray and interacting with volcanic rocks at a relatively low extent. In addition to volcanogenic gas inputs, the biogeochemical processes are influenced by microbial activities since the lakes offer specialized ecological niches for oxicand anoxic metabolism. The lakes were sampled in two extreme conditions of (partial) mixing (winter) and stratification (summer), respectively. The seasonal thermal stratification favored the development of anaerobic hypolimnia, showing relatively high concentrations of NH₄⁺ , NO₃^– , P and other minor species (Fe, Mn, Zn, As) controlled by microbial activity and minerogenetic processes occurring within the lake sediments. The strongly negative δ¹³ C-TDIC values measured in almost all the studied lakes suggest dominant contribution of organic carbon. Dissolved gases were mostly consisting of atmospheric compounds with significant concentrations of CO₂ and CH₄ . The δ¹³C-CO₂ values were intermediate between those measured in the hydrothermal fluids and those typical of biogenic CO₂. Dissolved CH₄ , which was the most abundant extra-atmospheric gas in the anoxic waters, was measured at significant concentrations even in the aerobic layers, especially in the winter season. This unexpected feature may tentatively be explained by admitting i) convective mixing of shallow and deep waters, and/or ii) aerobic CH₄ production. Further investigations, focusing on the recognition of microbial populations able to produce CH₄ at different redox conditions, may be useful to corroborate these intriguing hypotheses.