The present study analyzed the spatiotemporal changes of Ostracoda fauna in eight coastal lagoons in the Enez-Evros delta (Tuzla Lake 1, Tuzla Lake 2, Tuzla Lake 3, Taz, Işık, Dalyan, Kuvalak, and Taşaltı), located along the northern Aegean Sea coastline of Turkey. Recent ostracod samples collected from the eight lagoons were analyzed, and 16 living ostracod species (belonging to 14 genera) were identified during the sampling periods. The most abundant species were found to be Cyprideis torosa and Loxoconcha elliptica. C. torosa, a cosmopolitan and opportunistic species of Ostracoda, was found in all the studied coastal lagoons. All ostracod species determined in the lagoons were grouped into three assemblages: Group 1: halophilic continental freshwater species (F. fabaeformis, C. vidua, D. stevensoni, E. virens, H. salina, I. biplicata, I. bradyi, L. inopinata, and S. aculeata); Group 2: euryhaline and typical brackish water species (C. torosa and L. elliptica); Group 3: marine (coastal: A. convexa, L. rhomboidea, C. elongata, and X. communis) and brackish (lagoonal: L. lacertosa) water species. These species of Ostracoda were shown to be affected by environmental conditions. Analyses with the physicochemical variables and species (Spearman’s rank correlation coefficient and Canonical Correspondence Analysis) confirmed that ostracod distribution in the Enez lagoons are controlled by seawater–freshwater inputs and by salinity. The purpose of this work is about to present data about of the Enez lagoons, and analyze the diversity of ostracods of them.