The Water Framework Directive (WFD) aims at reaching good ecological status for surface waterbodies throughout Europe, by 2015. Consequently European countries are currently developing and intercomparing methods based on biological, hydromorphological and physico-chemical quality elements for the assessment and the monitoring of rivers, lakes, coastal and transitional waters. In this context, the FP7 WISER project aims to support the implementation of the WFD by contributing to making existing assessment methods more comparable. The present work focuses on fish indicators for estuaries and lagoons (transitional waters in the WFD). Six published fish indices were tested on a common dataset, covering eight estuaries and lagoons throughout Europe. Fish sampling was carried out using several gears in 2009 and 2010. The objectives were twofold: (i) to test the adaptability and the robustness of fish indices on different gears and different types of transitional waters; and (ii) to compare the behaviour of the indices with regard to their level of agreement and sensitivity to anthropogenic pressures. Five out of the six tested indices were gear-specific and all were specific to some type(s) of transitional waters. Therefore calculating the indices on the common dataset raised many difficulties, especially regarding the determination of reference values. However, it was possible to calculate most of the indices on most of the available data, thus showing their relative adaptability. The indication of extreme values for quality (high or bad) was rare and the results of the indices often differed. This shows that the assessment of quality using fish indicators is extremely dependent on the assessment tool, the sampling gear used and the type of transitional water body. Despite this, some common patterns in the diagnostics could be found hence requiring a possible intercalibration of the tested indices.