This chapter substantiates the essence, methodological approaches, and geo-information technologies of landscape-ecological monitoring (LEM) of lakes. It presents the results of the lakes LEM of the Nobel National Natural Park (based on the example of Lake Omyt). The research involved developing a landscape map of the key area, 'Lake Omyt,' and assessing the condition of its geo-complexes. The research also encompassed the development of a bathymetric model for Lake Omyt and the calculation of morphometric, hydrochemical, and hydrological parameters for the reservoir. Based on the geological sounding of landscape complexes of the lakeside terrace and bottom sediments of the reservoir, two reference sections (up to 5 m) and a stratigraphic section of sapropel deposits (up to 11 m) were made. The research also included evaluation of the geochemical characteristics of the bottom sediments of the lake. The proposed LEM algorithm for lakes in nature protection areas is effective and constructive; it can be used when setting up monitoring studies of other regions with a high level of lakes.