In a first biomarker-based study in Lake Baikal, we demonstrated that the heat shock protein Hsp70, a biomarker of exposure, is present in various endemic sponge species of the lake. The expression of Hsp70 was induced following heat stress in tissue or dissociated cells of the Baikalian sponges, Baikalospongia intermedia, Lubomirskia fusifera, and Lubomirskia abietina. Increased Hsp70 levels were still visible after a recovery period of 24 h. Exposure of B. intermedia to lead (Pb) and zinc (Zn) caused a strong induction of Hsp70 in this sponge, while copper (Cu) was not effective. However, all these heavy metals were able to induce DNA damage, a biomarker of effect, in B. intermedia, as determined by Fast Micromethod. Induction of DNA damage in B. intermedia was also observed after exposure to the organochlorines tetrachloroguaiacol and pentachlorophenol, which are released by pulp bleaching. The Baikalsk Pulp and Paper Plant (BPPP) is considered to be one main potential source of pollution of the lake. Investigations of the influence of the waste water from the final refinement and aeration pond of BPPP revealed a concentration-dependent increase in Hsp70 expression in B. intermedia. In addition, the effluents of the pond were able to induce DNA damage. The basal level of DNA single-strand breaks/alkali-labile sites in B. intermedia collected close to the site where the BPPP effluents are discharged into the lake was higher than that in sponges collected at an unpolluted site. Our results suggest that Baikalian sponges are suitable bioindicators to monitor water quality and ecosystem health of the lake.