An assessment is made of the hydrogeological situation on the industrial site of the Baikalsk Pulp and Paper Mill (BPPM) in the mode of operation of the enterprise. A profound transformation of the natural hydrogeochemical and thermal fields has been ascertained, resulting in the formation of contrasting (in mineralization, composition (sulfate and carbonate) and alkali-acid state)) groundwater with a temperature of 20–50 °C. The structure of the hydrogeochemical anomaly has been analyzed. It is ascertained that it undergoes intra-annual changes in the magnitude of mineralization and, partly, in composition. A series of discrete hydrogeochemical logging surveys showed that at the period of infiltration recharge the mineralization decreases to 1 g/L, and the composition approaches a sulfate-hydrocarbonate composition. During production shutdown intervals there occurs a clearly pronounced effect of piston-like displacement of polluted waters by the transit runoff: the maximum of mineralization is shifted right up to the discharge boundary, Lake Baikal. It is found that the transport of pollutants with the groundwater flow to Lake Baikal occurs with an attenuation in depth. Zonal experimental-seepage investigations showed that the profile totaling 50 m in thickness exhibits four approximately equivalent intervals with the effective velocity (from top to bottom) of 1.9; 0.84; 0.30 and 0.15 m/day. Thus it has been determined that 63 % of the most polluted groundwater flow is discharged trough the upper interval, and a mere 10 % through the two lower (least polluted) intervals. It is concluded that the liquidation of the BPPM will lead to the disappearance of the anomalies. Observations at regular intervals and specialized investigations from 1992–2013 testify that in the event that the pollution source is liquidated, the groundwater flow will be cleared of the polluting components to a local background level within a year.Keywords: structure of seepage flow, pollution sources, intra-annual variability in qualitative state of groundwater, thermal pollution, impact of the facility on Lake Baikal, forecast of changes in ecological situation.