Astroni volcano in the Campi Flegrei caldera (southern Italy) is a 2 km wide, densely vegetated tuff ring and hosting several volcanic structures, including tuff cones, scoriae cones, lava domes, and three small lakes. Geochemical data of waters and dissolved gases from the lakes, coupled with microbiological analyses on lake water and sediments, were used to shed light on the possible relationship between the lakes and the hydrothermal fluid circulation system as suggested by previous geophysical surveys. Water chemistry was dominated by solutes, mainly Na+ and HCO3−, deriving from fluids and CO2-rich gases typically found in discharges located at the periphery of hydrothermal-volcanic systems. Lago Grande (LG) lake showed an anoxic hypolimnion with abundant non-atmospheric dissolved gases, consisting of biogenic CH4 and CO2, the latter having a twofold origin, biogenic and hydrothermal. The occurrence of anaerobic methanotrophs coupled with the lack of hydrogenotrophic methanogenic archaea along the whole vertical profile of LG suggested that CH4 was mostly produced from degradation of abundant terrestrial organic matter within the deep lake sediments, and then consumed during its diffusion through the lake. Notwithstanding, the output rate of CH4 from LG surface was anomalously high relative to those commonly measured in lakes. Carbon dioxide from the hydrothermal source and produced by CH4 oxidation was partially fixed in the lake via the acetyl-CoA pathway. Accordingly, the CO2 fluxes from the LG surface were relatively low, in the range of those measured in volcanic lakes dominated by biogenic CO2. The dependence of the chemistry of the Astroni lakes on inputs from the Campi Flegrei hydrothermal system, besides on biogeochemical processes, offers a possible explanation for the anomalous increase of the LG water level occurred in the last years, which was not consistent with the recorded local rainfall but likely caused by an increasing hydraulic pressure related to the enhanced hydrothermal activity recorded at Campi Flegrei in the last decades. According to this hypothesis, the future evolution of the current volcanic unrest may govern the fate of the lake water level with important implications for the functioning of the precious Astroni ecosystem.