The hydrosphere represents about 71% of the total surface of the planet of which only 2.8% is represented by freshwater ecosystems. The ecosystem maintains a state of balance between the component populations, throughout its self-control function, maintaining the numerical variations of these populations within certain limits of sustainability. The exceeding of these limits could causes the balance disturbance by changing the structure and functioning of the ecosystem. The complex human activities influence the structure and functioning of ecosystems, transforming the environment and adapting it to its purposes. Microorganisms are present in all types of ecosystems, being endogenous, exogenous or transient due to contamination with various sources of pollution. Water is an essential natural factor of ecological balance increasingly exposed to microbial pollution. Indicators of fecal pollution are used to assess the degree of water contamination and to locate its origin. The continuous and uncontrolled usage of antibacterial agents that contributed to bacterial resistance determined/ caused pollution of aquatic ecosystems with antibiotic resistant microorganisms. The emergence of antibiotic resistant bacteria is predictable in any environment given that the use of antibacterial substances is constantly growing worldwide. Thus, antibiotic resistance induced in the aquatic environment can have an effect both on bacterial populations in the ecosystem and on human health. Aquatic environments are recognized as one of the reservoirs for the transmission and dissemination of antibiotic resistance. The main goal of this paper is to highlight the differences of bacterial communities from anthropogenic and natural aquatic ecosystems and to assess the potential impact they have on environment and human health. The study area focused on two lakes in Bucharest, Lake Morii (anthropic) and Lake Snagov (natural). Microbiological and molecular biology methods were applied for a bacterial communities’ characterization. The fecal indicators were quantified by Most Probable Number method. The identification and characterization of bacterial populations in both aquatic ecosystems (Morii Lake and Snagov Lake) were performed by Omnilog (Biolog, USA) and by iSeq100 (Illumina, USA) gene sequencing techniques from bacterial aquatic ecosystem. Antibiotic susceptibility was tested following CLSI recommendation.