Three coastal and three lagoonal sites located in Greece (Eastern Mediterranean) were selected to test and intercalibrate classification methods developed for benthic invertebrates ecological quality assessments. These methods were developed for the purposes of the European Water Framework Directive which is a European legislation adopted for the protection and improvement of the coastal and transitional waters. However, through testing these methods, this work addresses in general the issue of determining and comparing the ecological status of the coastal and transitional macrobenthic communities in Eastern Mediterranean ecosystems. Among methods tested were the biotic indices AMBI and BENTIX, the multivariate method M-AMBI and the biomass size structure index ISD in lagoonal sites only. ISD index is a rather new method developed especially for transitional ecosystems and in this contribution its performance is intercalibrated with the other benthic classification metrics. Comparison and intercalibration of the indices results in assessing the ecological quality status (EQS) are presented graphically and statistically performing the Kappa analysis. Results of the comparison and the indices' performance are evaluated based on the knowledge of the sites' environmental condition and baseline studies. Based on an extended dataset of coastal and transitional ecosystems benthic invertebrates, an evaluation of each index performance and effectiveness is attempted through an insight and comparative analysis of each methods' structure and design. Results showed that in these Eastern Mediterranean coastal sites the BENTIX index seems to give a more biologically relevant classification and gives a higher confidence level regarding the classification compared to the other indices. In the coastal areas AMBI showed a tendency for the "good" class classification, while the factorial M-AMBI gave more consistent results with the BENTIX. In the lagoonal sites the biotic indices tested were not proved efficient enough and the biomass based ISD index proved more appropriate for these ecosystems. AMBI showed the highest agreement with the ISD which is due to the better performance of this index in the slightly and moderately polluted lagoons, compared to the other indices. However, AMBI failed to classify the polluted lagoon, in which case the BENTIX gave a more relevant classification.