As concerns field work, bathymetric measurements as well as measurements of physical and chemical parameters of water were conducted, and samples were collected for laboratory tests, which included quantitative and qualitative hydrobiological analyses concerning e.g. the abundance, biomass and species composition of phytoplankton, seston and chlorophyll. Six water bodies (situated in flooded chalk pits) with different morphometric parameters (areas ranging from 2.22 to 37.67 ha, depths ranging from 5.1 to 23.0 m and nearshore shallow areas ranging from 0.39 to 2.64 ha) and with different bioproductive characteristics of water mass (eg. transparency – 1.2–6.8 m, phosphates – 0.002–0.110 mg/dm3, nitrates – 0.040–0.600 mg NO-3/dm3, biomass of phytoplankton – 0.075–1.801 mg/dm3, seston – 0.73–5.56 mg/dm3) were selected for the study of the phytomediation mechanism. The specificity of structural and functional relationships between the abiotic and biotic components of productive-macrophyte and productive-phytoplankton reservoirs is determined. It was established that macrophyte water bodies in flooded chalk pits are able to maintain their basic production and trophic characteristics in the long term under anthropogenic influence conditions. An algorithm is proposed for calculating the level (E – 89.58–115.13), productivity index (K – 11.16–54.15) and gradient (E – 2.1–9.8) of eutrophication of chalk (limestone) quarry reservoirs using the morphometric specificity indicator of the trophogenic epilimnial layer (Sτ – 0.05–0.270). The revealed dependence of the productive and functional organization and trophic status of a quarry reservoir on the morphometric features of a technogenic basin is proposed to be used in the design of sustainably functioning macrophyte-type aquatic systems at the stage of mining and engineering reclamation. The possibility of creating ecologically sustainable lake-type aquatic systems on the site of resource depleted chalk quarries in the process of phytomediation of productive processes is substantiated. Research on innovative methods of reclamation of flooded chalk pits is in line with several sustainable development goals.