The Adriatic Sea is a semi-enclosed sea and its ecosystem is influenced by the regular exchange of water with the Eastern Mediterranean. Levantine Intermediate Water and Ionian Surface Water flow into the Adriatic along the sea’s eastern border. The volume of this flow depends on climatic oscillations that occur from the Atlantic to the Southeast Mediterranean. The South Adriatic, the deepest part of the Adriatic Sea, represents a key area for both the Adriatic Sea itself and the entire Eastern Mediterranean basin. Tintinnids are the best known ciliates in the marine plankton. Their high frequencies and identifiable morphology have been suggested as indicators of oceanographic conditions including water temperature and origin, such as neritic, oceanic, and even upwelling water. Samples in South Adriatic were collected at four stations with a 53 µm mesh Nansen net. The spatial and temporal distribution of tintinnids was investigated at monthly intervals in the South Adriatic Sea during 2016. Of the 68 species identified, there were 47 surface, 15 subsurface, 3 mid-water, and 1 deep sea species. The dominant surface and subsurface species were Codonella aspera, Codonella amphorella, Undella claparedei and Salpingella accuminata. Species Parundella lohmanni predominated in the mid-water layers and Xystonellopsis scyphium in the deep-sea layers. While the majority species are always present in the South Adriatic Sea, some species were occasionally immigrates from the Mediterranean Sea. The highest variability in the number of species occurred in the surface and subsurface layers. A mid-water community of species Parundella lohmanii indicated inflowing South Adriatic Deep Water. Some other species such as Poroceus apiculatus, Undella subcaudata and Eutintinnus elegans appeared with strong inflows of the Levantine Intermediate Water during winter and spring. Based on these results, tintinnids may be used as a biological indicator of the state or possible changes in the marine ecosystems of the South Adriatic Sea.