We survey the diversity of antimicrobial resistance profiles of Escherichia coli ( E. coli) isolates and molecular genotypes by means of phylogenetic groups circulating in the environment, in sewage and receiving waters bodies as well as clinical isolates both from Boeotia regional district of Greece. The predominant resistant profile among all environmental isolates was to penicillins - ampicillin (AMP) and piperacillin (PIP). ESBLs resistance related profiles were observed both in environmental and clinical isolates. Phylogenetic group B2 was the predominant in clinical isolates, whilst group A was dominant in environmental isolates. We report that reclaimed river water and wastewater are reservoirs of R and MDR E. coli to commonly used antibiotics in clinical practice posing putative threats for human and animal health.