Semi-enclosed bays are generally considered important environmental resources for mariculture. This study was conducted within cage fish farms in two semi-enclosed bays of the Eastern Adriatic Sea, at Boka Kotorska Bay (Montenegro), and at Mali Ston Bay (Croatia). A total of 16 sea water samples, and 46 swabs from the gills and skin of European seabass were collected from two sea bass farms during two samplings in autumn and spring. The aim of this study was to determine the health status of European seabass in Montenegro and Croatia, to evaluate the environmental conditions in both farming areas, and to assess the presence of Vibrio and its impact on fish health. Most of the isolated bacteria from the samples were Gram-negative and comprised of Vibrio, Photobacterium and Pseudomonas genera. Assessment of fish health status showed that fish were clinically healthy and results present a bacterial community associated with healthy farmed European seabass. At the same time, some of the isolated bacterial strains are known to be pathogenic (V. alginolyticus, V. harveyi, V. anguillarum, P. damselae), and present a potential reservoir of infection. Simultaneous survey confirmed microbial impact in both bays due to an anthropogenic influence. The approach presented in this study is valuable in the assessment of farming conditions in semi-enclosed aquatic environments and is easily applicable to other similar locations worldwide.