Abstract This paper aims to test the suitability of some biotic indices for their application in Southeast Caspian Sea. For this purpose, the ecological quality of the Gomishan lagoon was assessed using three biotic indices (AMBI, BENTIX, BOPA) during summer and autumn 2010. The results from the application of the biotic indices do not highlight a clear distinction between the stations. The results show that two of the indices (AMBI and BENTIX) are very close in terms of diagnosis (good and high) and seem to generally perform better than BOPA. In addition, Principal Component Analysis (PCA) based on abiotic parameters showed clear spatial and temporal differences in environmental variables. However, at this shallow sites with low human pressure and high water residence times, such benthic community composition can be associated with physical stress due to salinity increase and to changes in environmental characteristics, triggered by conventional seasonal variations. Natural variability of transitional waters is a crucial factor for a correct evaluation of the ecological condition of macroinvertebrate communities across the lagoonal system.