Estuary areas are of great ecological, aesthetic, economic and cultural importance and as such are among the most productive and dynamic ecosystems on Earth. Due to specific conditions such as the mixing of water masses of different salinity and the abundance of nutrients present in the area, estuaries are considered very important habitats for many types of terrestrial and aquatic organisms, which makes them habitats with an extremely high biological diversity. An example of such an area is located on the west coast of Istria, known as the Lim Bay. The inner area of the Lim Bay is strongly influenced by underwater freshwater springs, which makes it an extremely biologically productive area. In this research, hydrographic parameters were monitored - temperature, salinity, pH value and oxygen saturation, and microbiological indicators such as the abundance of the marine microbial community, and sanitary control of the sea was carried out through four seasons. The hypothesis about the significant influence of underwater freshwater springs on hydrographic parameters and the abundance of the microbial community in the surface part of the bay, and the hypothesis that coastal underwater freshwater springs in the Lim Bay represent a potential source of fecal bacteria, were confirmed by the obtained results. Based on the conducted research, it can be concluded that in the coastal part of the Lim Bay, the inflow of fresh and cold water through underwater freshwater springs leads to changes in hydrographic conditions, which creates specific ecosystem conditions that are suitable for the heterotrophic component of the microbial community. In addition, the occasional presence of higher concentrations of fecal indicators in fresh water from underwater freshwater springs negatively affects the sanitary quality of the sea in the bay. It is necessary to carry out regular sanitary controls of the sea and precisely identify and remediate the sources of fecal pollution in order to protect this special reserve in the sea from anthropogenic pollution.