Listvennichnyi Bay is one of the most anthropogenically altered areas of South Baikal in terms of algal benthic communities. A sanitary–bacteriological and hydrochemical survey was conducted in four tributaries of the bay near the Listvyanka settlement (about one million visitors per year!) from 2014 to 2019. Sterile gloves, syringes, and sterile bottles were used for sampling. A specially elaborated device with two syringes was applied for bottom water sampling. The methods of filtering samples through nitrocellulose filters and the subsequent sprouting of bacteria on selective media were used for microbiological analysis. Nutrient analyses (phosphate-P, ammonium-N, and nitrite-N) were performed with a spectrophotometer. The concentrations of nitrates were determined by high-efficiency liquid chromatography with indirect UV detection. Our findings indicate that the water quality at the mouths of Bol’shaya Cheremshanka, Malaya Cheremshanka, and Kamenushka rivers falls below Russian standards for thermotolerant Escherichia coli and Enterococcus spp. Additionally, these locations failed to meet Russian standards for hydrochemical parameters like phosphates. Our study indicates a significant disparity in water quality between the river mouths and upstream reaches near the settlement. The stable inflow of additional nutrients with polluted riverine waters is one of the most important reasons for the mass development of filamentous algae of Spyrogira genus nontypical for Baikal, which leads to disruption of the typical algal belts and unique zoobenthos communities in the coastal zone. Besides, the poor water quality prevents recreational use of the lower parts of the tributaries and coastal zone of the bay.