The coastal area of the southern Lake Baikal with the population over 35,000 people remains an attractive spot for both tourists and local residents. Despite high anthropogenic impact, a detailed assessment of water quality in this area has not been performed so far. Here, we performed a comprehensive evaluation of the quality of the surface, bottom and interstitial water in rivers, lacustrine water and wastewater in the southern Lake Baikal region. We analyzed 37 samples for the presence of fecal enterococci, Escherichia coli and assessed their hydrochemical parameters: concentrations of nutrients (nitrate-N, nitrite-N, ammonium-N and phosphate-P), dissolved oxygen and amount of ions (HCO3- + SO42- + Cl- + Ca2+ + Mg2+ + Na+ + K+). In addition, the temperature, pH and electrical conductivity were also measured. We found that multiple areas around South Baikal suffer from microbiological and hydrochemical pollution. We conclude that ecological situation in this area requires immediate attention from local authorities, more efficient wastewater management systems should be constructed in the settlements. We also conclude that interstitial waters from the lake's splash zone represent an effective and sensitive indicator of sanitary-microbiological and hydrochemical pollution and their analysis can be included in the standard protocol of water quality assessment for all types of water bodies.