In 2014–2016 complete parasitological autopsy was used to examine 202 individuals of the Kura River estuary fish, belonging to the following 14 species: Caspian common sprat – Clupeonella delicatula caspia, Caspian shad – Alosa caspia caspia, black-backed shad – A. kessleri kessleri, Caspian roach – Rutilus rutilus caspius, kutum – R. frisii kutum, asp – Aspius aspius taeniatus, Kura shemaya – Chalcalburnus chalcoides, Transcaucasian silver bream – Blicca bjoerkna transcaucasica, bream – Abramis brama orientalis, Caspian vimba – Vimba vimba persa, carp – Cyprinus carpio, catfish – Silurus glanis, pike – Sander lucioperca, perch – Perca fluvistilis. As a result of the research there were found following 21 species of parasitic protozoa belonging to 5 phyla, 7 classes, 7 orders and 8 families: flagellates Trypanosoma carassii, Cryptobia borelli, Costia necatrix, coccidia Eimeria carpelli, microsporidium Pleistophora siluri, myxosporeans Myxobolus bliccae, M. bramae, M. cyprini, M. dispar, M. ellipsoides, M. muelleri, M. musculi, M. oviformis, M. pseudodispar, M. rotundus, infusorians Chilodonella hexasticha, Ch. piscicola, Ichthyophthirius multifiliis, Trichodina caspialosae, Ichthyophthirius multifiliis, Trichodina caspialosae, Trichodinella epizootica. The most frequent organ of localization of the parasites were the gills, in their tissues 7 species of myxosporeans, and on their surface 1 species of flagellates and 6 species of infusorians were found. In each of the remaining organs there were noted following numbers of species of parasitic protozoans: in the kidneys – 9 species, in the spleen – 7 species, in the muscles of the body – 6 species, in the skin and bladder – 5 species, in the liver – 4 species, on the surface of fins, in the bloodstream, intestinal walls and gall bladder – 2 species, in the heart, subcutaneous connective tissue, eyes and brain – 1 species. In the composition of protofauna, endoparasites (14 species) significantly prevailed over ectoparasites (7 species), and the forms that develop with a change of hosts (12 species), prevailed over forms that have a simple development cycle (9 species). Most of the parasites are of freshwater origin, so more species of parasites were found in fish caught in the highly desalinated part of the Kura estuary than in areas with more mineralized water. It has been established that, in contrast to ectoparasites, freshwater endoparasites, the infection by which occurs in fresh water, in the body of fish are also transferred to more mineralized sites. Among all discovered protozoa 7 species are the causative agents of fish diseases. However, due to not very high infection of fish, no pathogenic phenomena caused by these parasites were observed.