Recent studies have revealed how the freshwater biota of Lake Baikal responds to climate change and anthropogenic impacts. We studied phyto- and zooplankton, as well as phyto- and zoobenthos, in the open coastal waters of the southern basin of the lake and of Listvennichny Bay. A total of 180 aquatic organism taxa were recorded. The response of the Baikal ecosystem to climate change can be traced by changes in the species composition of planktonic communities of the lake’s open coasts in summer. The key species were thermophilic the Anabaena lemmermannii P. Richt. (F_ij = +0.7) blue-green algae, the Asplanchna priodonta Gosse (F_ij = +0.6) rotifers in 2016, the Rhodomonas pusilla (Bachm.) Javorn. (F_ij = +0.5) cold-loving algae, and the Cyclops kolensis Lilljeborg (F_ij = +0.9) copepods in the past century. The proportion of Chlorophyta decreased from 63% to 17%; the Cyanophyta increased from 3% to 11% in the total biomass of phytoplankton; and the proportion of Cladocera and Rotifera increased to 26% and 11% in the biomass of zooplankton, respectively. Human activity makes an additional contribution to the eutrophication of coastal waters. The Dinobryon species, the cosmopolitan Asterionella formosa Hass. and Fragilaria radians Kütz., dominated phytoplankton, and filamentous algae, Spirogyra, dominated at the bottom in the area with anthropogenic impact. The trophic level was higher than at the unaffected background site: the saprobity index varied from 1.45 to 2.17; the ratio of eutrophic species to oligotrophic species ranged from 1:2 to 3:1, and the ratio of mesosaprobiont biomass to endemics biomass ranged from 2:1 to 7:1. Currently, the boundaries of eutrophication zones of shallow waters in Lake Baikal are expanding, and its coastal zone has acquired features typical of freshwater bodies of the eutrophic type.