Estuaries are unique habitats where organisms can find food, a place to reproduce, and protection from predators. The main factors which affect the living world in the estuary are salinity, sedimentation, and dissolved nutrients. Salinity is variable and depends on the level of mixing of fresh and salt water. Rivers bring large amounts of material, and the most common types of sediments covering the bottom of the estuary are sand and silt. Changes in physicochemical factors are common, and few organisms can fully adapt. Some of the most important adjustments are the ability to osmoregulate and attach to the soft bottom. Many organisms bury themselves in sediment or swim away under unfavorable conditions. Plants at the edges of the estuary can store large amounts of water in their tissues or excrete excess salt through the salt glands. The estuary harbors photosynthetic organisms that ensure primary production throughout the year, with large amounts of nutrients being brought in by the rivers. Increased concentration of nutrients in the estuary has harmful consequences such as hypoxia, anoxia, harmful algae blooms, and biodiversity loss. Estuaries are areas under the significant anthropogenic influence, and eutrophication is often present. Silicon, nitrogen, and phosphorus have the most significant contribution to the eutrophication of estuaries. Organisms use silicon to build their shells. Phosphorus is introduced through sewage and agricultural products. Nitrogen can enter as a by-product of wastewater treatment or from the atmosphere. We find numerous bays and highly stratified karst estuaries in the Adriatic Sea, enriched with inorganic and organic substances. They are created by karst rivers in areas where the change of tides is not significant. These ecosystems are unique in their features and characteristic of the karst coastal area of the Republic of Croatia. They need to be studied to contribute to their adequate protection and sustainable use.