Deltas are reservoirs for important plant and animal species and have a vital role in maintaining sustainability of ecological balance. In addition, because of anthropogenic pressure they are recognized as natural habitat of pathogenic microorganisms and infectious diseases caused by these bacteria are dangerous to aquatic animal's health and could potentially affect several species as well those are endangered. This study aims to determine the micro-flora of freshwater turtles (Emys orbicularis Linnaeus, 1758 and Mauremys rivulata Valenciennes, 1833) and sensibilities of these turtles against isolated pathogenic bacteria. Furthermore the investigation was conducted to characterize diseases causative agents. Their risks to animal and human health are difficult to carry out, especially for some turtle species. The results showed that the isolates were identified as Vibrio spp. and Proteus spp. So, these bacteria are the main pathogens isolated from E. orbicularis and M. rivulata. These data appoint the importance of epidemiological surveillance and microbiological monitoring and reinforce the need to implement environment protection programs especially for the threatened turtle species (E. orbicularis).