In this study, the evaluation of limnochemical aspects, as well as the study of the microbial trophic network (protozooplankton and bacterioplankton) belonging to the uranium mine acid lake (CM) and the assessment of possible effects of acidic effluents treated and released by the UTM/INB into the Ribeirão das Antas Sub-Basin of the Antas reservoir (P41) and into its downstream -the Bortolan reservoir -were conducted. In addition to the execution of a series of physical and chemical analyses and quantification of protozooplankton and bacterioplankton, the standardization and implementation of the independent technique of Fluorescent In Situ Hybridization -FISH -was conducted using oligonucleotides probes stained with Cy3 for bacteria detection of the domains Archaea and Bacteria, both for the uranium mine acid lake and for the reservoirs. According to the results observed in this study, CM presented the highest values for the chemical variables evaluated, the lowest pH values and the least diversity and density of protozooplanktons. However, it presented high protozooplanktonic biomass, demonstrating the presence of species tolerant to such extreme environmental conditions. The Antas and Bortolan reservoirs presented differences in relation to abiotic and biotic variables; the RA indicated greater interference from the acidic effluents treated and released into point P41, and on its downstream, point P14, presenting less protozooplankton biomass, lower bacterial density, lower trophic state index and sources of pollution characteristic of inorganic sources, probably due to flaws in the treatment system of the effluents released into this reservoir. On the other hand, RB presented higher trophic state index, higher density and biomass of both protozooplanktons and bacterioplanktons, greater values for chlorophyll a concentrations, nutrients and sources of pollution characteristic of organic origin -probably due to its proximity to the urban area of the city of Poços de Caldas. Through the use of the refined FISH technique in this study, for the water bodies assessed, it was possible to detect the presence of microorganisms of the Archaea and Bacteria domains in the three water bodies assessed. Thus, the results of the current study contribute to the knowledge, at a limnological level, of open pit lakes (which have become a source of great concern due to the increase of mining operations), as well as the detection of possible effects of acid and radiological effluents released into the environment.