The effect of the modifications of the threshold values generally adopted for the five EcoQ (Ecological Quality) classes recognized by the European Water Framework Directive (WFD) for the most used benthic indicators and diversity indicators (AMBI, BENTIX, BOPA, BQI, H', ITI and M-AMBI) were studied to test whether it is possible to obtain the same or similar ecological classifications for transitional waters using these different indicators, and determine whether the current classifications can be improved. The analysis included: (i) the use of indicator equations, (ii) the use of reference indicators, and (iii) the use of indicator distribution laws. These investigations demonstrated that it was impossible to obtain an exact intercalibration of the ecological classifications with the selected indicators. However, some propositions to improve the actual classification were suggested.