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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 oxic and 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 d13C-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 d13C-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.