Numerous active and fossil hydrothermal carbonate chimneys have been reported at Lake Asal and Lake Abhe, in the southeastern part of the Afar Rift (Republic of Djibouti): a tectonically and volcanically active region for the last 30 million years. In this study, we report on a detailed mineralogical and geochemical investigation of unusual hydrothermal mixed carbonate-siliceous chimneys recently discovered in the Allols area (Harralol, Haralé Awda and Sakallol), northwest of the Asal Rift. These inactive chimneys, up to 20 m high, consist of tall spires partly stained by Fe-oxides. They are located along major faults and were formed sub-aqueously when the area was occupied by a lake. Hydrothermal carbonate structures were also found in the same area. The oxygen (δ18O) and carbon (δ13C) isotopic compositions of the chimneys range from −4.5 to 25.3‰ and from −9.44 to 8.92‰, respectively, indicating mixing between magmatic and surficial waters. Their radiogenic Sr isotopic compositions (87Sr/86Sr = 0.7049–0.7056) show values typical of altered basaltic rocks. Chimneys also exhibit negative Ce anomaly suggestive of a genetic link with basalt alteration. Overall, this study suggests that lake water chemistry in the Allols area experienced major changes in the past, reflecting various contributions of mixing fluids (lake water and hydrothermal fluids), leading alternatively to deposition of carbonate chimneys and precipitation of (and/or replacement with) silica.