Although wetlands have been viewed as worthless and unnecessary areas for centuries, this attitude has gradually changed in recent decades. Today, wetland ecosystems are recognized as very valuable habitats due to their extremely high productivity and the richness of species, from the smallest microorganisms to plants and animals. The aim of this research is to investigate the seasonal dynamics of the indigenous microbial community and fecal bacteria in the special hydrographic conditions of the waters of the Palud salt marsh and compare it with the marine microbial community in the immediate vicinity of the marsh. The area of the special ornithological reserve Palud - Palù is of special importance for all organisms that live in that area, and the marsh located in the very center of the reserve is a specific ecosystem in the area of the northern Adriatic. Sampling was carried out at 9 previously determined stations, in the area of the special ornithological reserve Palud - Palù and took place 7 times in the period from the end of July 2021 to May 2022. The sanitary quality of the water and the abundance were determined autochthonous microbial communities in the marsh, the sea and in the marsh channel that connects the marsh with the sea. A statistical analysis of the data was also made to show the correlation between seasonality and measured abiotic factors, as well as the grouping of stations depending on the sampling position and depending on the presence of indicator microorganisms or autochthonous microbial communities. During the warmer months (summer 2021 and spring 2022), the concentration of fecal pollution indicators, as well as the abundance of the autochthonous microbial community, was expected to be higher than during the colder months (autumn 2021 and winter 2022). The obtained results were compared with average data for the northern Adriatic available in the literature, as well as with long-term data averages for station RV001 at 1 NM west of Rovinj. The results showed that hydrographic parameters in the marsh have large seasonal oscillations, but also that sea changes play an extremely important role in the functioning of the microbial community and the entire ecosystem.