Vibrio populations in the seawater supply and the water of seven exhibition aquaria that simulate various Mediterranean and tropical ecosystems were compared. The similarity of Vibrio populations in the intestine of various fish species, feed and water was examined. Resistance to the antibiotics used in fish health management was analysed for the dominant Vibrio isolates. Samples were collected for 1 year from seven exhibition tanks reproducing different ecosystems. The diversity and population similarity among vibrios were determined using a miniaturized biochemical phenotyping method. Similar Vibrio populations were found in the water supply and in the water of the Mediterranean ecosystems. However, different Vibrio populations were found in the water of tanks with tropical ecosystems. Vibrio populations in the water seemed to have a greater effect on the composition of intestinal Vibrio populations than those in feed. No resistance to antibiotics was observed, indicating their appropriate use for health management. Water characteristics have a greater impact on the composition of Vibrio populations in aquaria and fish intestinal microbiota than bacteria in feed. The microbiological monitoring water could provide valuable information for managing the health of exhibition aquaria.