Advances in IT (information technology) and the availability of electronic equipment are the reason for the increasing adoption of underwater cameras in marine fauna research. The listed reasons allow continuous monitoring and a better understanding of the functioning of the marine environment. In this study collected underwater images in the Krka estuary (Natura 2000 locality - HR3000171) were analyzed. Monitoring of the seasonal presence and frequency of occurrence of marine fauna was performed during January, April, July and October of 2019. All underwater images were collected daily from sunrise to sunset, where 54 species of marine fauna represented by 55,612 individuals were determined. Among all the recorded species, the most abundant were fish (82 % in regard to others). Additionally to the ichthyofauna, shag (Phalacrocorax aristotelis), loggerhead sea turtle (Caretta caretta) and several species of invertebrates (two species of starfish, three species of cephalopods, one crustacean and one bivalve mollusc) were recorded. Economically important species represented 72 % of all species. The canonical correspondence analysis (CCA) indicates a pronounced seasonal appearance of some species (especially noticed in the species of the genus Spicara and the European sea bass, Dicentrarchus labrax) which may be related to their ethological properties, feeding and spawning. The results of this work may contribute to a better understanding of the ecosystem biodiversity of the studied area and can serve to define the guidelines for the future management plan of this important area of the Natura 2000 ecological network.