We report results of bottom temperature monitoring of 2003–2004 in the deepwater South Baikal basin (Lake Baikal) near active gas-fluid methane vents at lake depths of 1020 and 1350 m. Sediments and water temperatures were measured using an autonomous temperature recorder designed at the Institute of Geophysics (Novosibirsk). Experiments implied short-duration recording and pioneering continuous 350 day-long monitoring near the Staryi vent. Measurements within a 1 m thick layer above and below the bottom showed notable variations in water (up to 0.07 °C) and sediment temperatures and in geothermal gradient. The long temperature records include a relatively steady period (mid-June 2003-early February 2004) with smooth temperature variations (especially in sediments) and two transient unsteady periods. The steady season is the best time for heat flow studies in the South Baikal basin. The 0.04–0.05 °C drop in bottom water temperature during the unsteady periods may result from intrusion of cold surface water. A positive temperature anomaly of ∼0.04 °C recorded in April 2003 may be caused, among other reasons, by active gas venting.