Hydroelectric dams create new ecosystems such as reservoirs. Several hydroelectric dams forming shallow reservoirs were built on the Angara River flowing out of Lake Baikal. The first of them in downstream Angara is Irkutsk Reservoir, with several shallow bays. Since silica-scaled chrysophytes are effective bioindicators for aquatic ecosystems, this paper aimed to determine their distribution, taxonomic structure and species richness in South Baikal and Irkutsk Reservoir, which have different environmental parameters. Thirty-one species were found using scanning and transmission electron microscopy. Only seven of them inhabited South Baikal in June 2023 at 3.66–4.51 °C and pH 7.80–8.24, with Chrysosphaerella baicalensis, Spiniferomonas trioralis f. cuspidata and Mallomonas alpina being prevalent. Only one species (M. alpina) was dominant in Irkutsk Reservoir at all stations at a water temperature of 5.33–11.55 °C and pH 8.10–8.52, alongside three other abundant species, Synura cf. glabra, Mallomonas acaroides and M. crassisquama. The maximum number of species (23) was found in a shallow bay of the reservoir at maximal values of temperature (11.5 °C) and pH (8.57) and minimal values of phosphate and nitrate concentrations during the study. The enrichment of Irkutsk Reservoir in species of silica-scaled chrysophytes was due both to cosmopolitan widespread and polyzonal species as well as to rare boreal, arctic–boreal, and unknown, possibly new species.