The study area consists of wetlands and semi-wetlands (saltpan and salt lakes) that are separated from the Gulf of Saros in the northeastern Aegean Sea by a littoral cordon. Twenty-four samples were collected from the Enez Salt Lake; Dalyan, Enez Gala, Kuvalak, Isik, and Tasalti Lakes; Vakif and Erikli Saltpans; and Karagol Lagoon. The overall distribution of the sediment sizes reveals that they consist predominantly of mud and sand and a mixture of mud, sand, and gravel. The average proportion of gravel size particles is 8.36%. Feldspar and mica are abundant in sand and gravel-sized materials. Ecological conditions of these coastal areas were assessed on the basis of ostracod assemblages that can be considered as useful bioindicators and depend on water depth, temperature, and salinity. In this context, the effects of physical and chemical properties of the environment, geochemistry of the sediment, and anthropogenic impact on the meiofauna, in particular ostracoda, was here evaluated. Cyprideis torosa Jones, a cosmopolitan species of ostracoda, was found in salt lakes. Other species of ostracoda were shown to be affected by environmental conditions. The toxicity of some heavy metals in the saltpans, salt lakes, and hypersaline lagoons was evaluated. Lake Dalyan and Erikli Saltpan display high toxicity for Cu and Cd levels. The distribution of hydrocarbon pollution of terrestrial origin was determined. © 2015 Firat University Scientific Research Projects Management Unit This work was supported by Scientific Research Projects Coordination Unit of Istanbul University . Project number: BAP-179/15012004 . The authors would like to thank Assistant Prof. Dr. Selma Unlu (Istanbul University) for conducting the TPH analysis. The authors express their sincere gratitude to the following persons: Mr. Murat Dundar (General Director of ASSAN Ar-Ge) and Technician Husnu Ozturk (ASSAN Ar-Ge) for providing the photographs that were taken by using Jeol-JSM electron microscope; Dr. Nazlı Demirel (Istanbul University) for his contribution to the statistical analysis; and to Emine Şeker (PhD student at Çukurova University) for scale added to Plate. In addition, we thank Dr. Gilles Carbonnel and the unknown reviewer for their valuable comments on the manuscript. Finally, a special thanks goes gratefully acknowledge editorial help to Dr. Eric Armynot du Châtelet and Dr. Maria-Angela Bassetti, as well as the editor-in-chief Dr. Taniel Danelian for their thorough review and constructive suggestions.