It has been observed the spread of a growing number of antibiotic resistant bacteria (ARB) outside the clinical setting into the environment. The surface water seems to play an important role in ARB dissemination by being both habitats and transport systems for microorganisms, respectively. The ecological and touristic importance of the Danube Delta make it an European priority for a close observation and monitoring of its freshwater system. The main goal of this paper was to analyze how the St. Gheorghe branch of the Danube Delta microbiological contamination and their antibiotic resistant profile were influenced by climate change, especially the global warming from 2013 up to 2019. The bacterial population’s analyses revealed an indirect proportionality between coliform bacteria density in water and sediment during the time. Bacterial strains resistant to commonly used antibiotics in clinical settings were more and more identified and the strains exhibited high rates of beta-lactam resistance, especially to ampicillin and amoxicillin enriched with clavulanic acid.