We examine the complicated situation with demarcation of the boundary of the Lake Baikal water protection zone. It was found that although the principles of ecological zoning, a unique legal instrument regulating the development of a territory with a special nature conservation status and the preservation of the Lake Baikal ecosystem, have been developed and implemented, it was not until 2015 that the boundaries of the water protection zone of Lake Baikal itself were defined. The boundaries of the water protection zone along the boundary of the central ecological zone of Lake Baikal as established by a Decree of the RF Government combined severe restrictions on water use of the two zones across the territory with the area more than 50 thou km2. It is concluded that there is a need to reconsider the decision and develop the project of the water protection zone of Lake Baikal substantiated from the landscape-hydrological perspective. It is demonstrated that the substantiation of the size of the water protection zone must rely on the hydrological runoff-forming and runoffregulating functions of landscapes that determine the formation and transformation of the local runoff between the watershed and the draining water body. The approach to implementing the water protection zoning project on the landscape-hydrological principles is developed to provide maximum protection of Lake Baikal against the input of pollutants with the subsurface and surface runoff from the neighboring coastal territories due to the natural processes of self-purification in landscapes and soil-ground layers. The main criterion is defined for the width of the water protection zone: all pollutants beyond the imposed limits of the zone are drained by the inflows from the lake and do not enter directly Lake Baikal; also, the protection of subsurface waters from the vertical penetration of pollutants is taken into account. For the settlements situation on the shores of Lake Baikal, it is proposed to delineate the boundary of the lake’s water protection zone having regard to the existing and future plans of development and engineering-technological infrastructuring of the territory.