Coastal lagoons are shallow, complex habitats defined by fluctuations in salinity and temperature. Due to its complexity, these rare and endangered ecosystems are protected under directives of European Union, as a part of the Natura 2000 ecological network. Makirina bay and Morinje inlet represent shallow coastal lagoons of the eastern coast of the middle Adriatic, whose sediment floor is made of fine, peloid mud. Water column between surface and nutrient rich sediment floor is covered with phytoplankton communities that, proposed as bioindicators, provide information on the ecological status of two coastal lagoons. An investigation of the ecological condition of the two coastal lagoons was carried out in the spring and summer of 2018 as a part of the project "Preparation of expert background for nature protection for the use and exploitation of the area of the NATURA 2000 ecological network in the area of Makirina bay and Morinje bay" (Oikon Ltd. - Institute of Applied Ecology, 2018) to establish the ecological status of two coastal ecosystems, compare the phytoplankton community and assess the existence of indicators of eutrophication. The composition of the phytoplankton in the bay of Makirina and Morinje inlet is very similar and ecosystems are dominated by diatoms and small nano fraction dinoflagellates. The dominance of the dinoflagellate Prorocentrum species suggests a very eutrophic state of both ecosystems and great anthropogenic influence. The observed species of Alexandrium indicates to the toxicity of the phytoplankton. Although the descriptors of coastal water quality according to the EU directives do not include phytoplankton composition, the results of this study indicate that the composition of phytoplankton is a very good indicator of trophic levels and the ecological status of coastal ecosystems, and points out the need to include phytoplankton composition in the list of water quality indicators under the EU directives.