The article, using the example of the territories of the Troitsky and Novomoskovsky administrative districts (hereinafter referred to as TiNAO) of Moscow, shows the possibility of a geoecological assessment of changes in the morphometric parameters of small reservoirs. Before joining the administrative structure of the Moscow territories in 2012, the studies on the ecology of these territories was minimal. Of particular importance for monitoring the geo-ecological situation in “New Moscow», – what the conjoined territories are also called, is the fact that its area is 1,480 km2, which is 57.8% of the entire territory of Moscow. The subject of the study were 1402 small reservoirs registered in the territory of the TiNAO. To carry out their environmental assessment, a cluster analysis method was used, which is a universal mathematical tool for scientific research. A negative change (decrease) in the average depth of the reservoir was taken as the main parameter of the study. Based on the results of the objects’ morphometry analysis carried out at an interval of two years, data on dynamic changes in the physical parameters of reservoirs were obtained and processed. It was established that shallowing problems exist in 4.51% of the total area of reservoirs in the TiNAO. Mapping stagnant small reservoirs made it possible to visually assess the scale of the problem and identify potentially problematic areas of the TiNAO from a geoecological point of view. Using the cluster analysis, zoning of problematic water bodies was carried out. Such identification (clustering) of water bodies’ grouping made it possible to see deviations at the level of groups of small river basins, which provided a large-scale understanding of the ecological situation at the level of catchment areas of larger water bodies.