This paper exposes a newmethodological approach to solve the problemof intercalibrating river quality national methodswhen a common metric is lacking and most of the countries share the sameWater Framework Directive (WFD) assessmentmethod.Weprovide recommendations for similar works in future concerning the assessment of ecological accuracy and highlight the importance of a good common ground to make feasible the scientific work beyond the intercalibration. The approach herein presentedwas applied to highly seasonal rivers of the Mediterranean Geographical Intercalibration Group for the Biological Quality Element Macrophytes. TheMediterranean Group of river macrophytes involved seven countries and two assessment methodswith similar acquisition data and assessment concept: theMacrophyte Biological Index for Rivers (IBMR) for Cyprus, France, Greece, Italy, Portugal and Spain, and the River Macrophyte Index (RMI) for Slovenia. Database included 318 sites of which 78 were considered as benchmarks. The boundary harmonizationwas performed for common WFD-assessment methods (all countries except Slovenia) using themedian of theGood/Moderate andHigh/Good boundaries of all countries. Then,whenever possible, the Slovenianmethod, RMI was computed for the entire database. The IBMR was also computed for the Slovenian sites and was regressed against RMI in order to check the relatedness of methods (R2=0.45; p b 0.00001) and to convert RMI boundaries into the IBMR scale. The boundary bias of RMI was computed using direct comparison of classification and the median boundary values following boundary harmonization. The average absolute class differences after harmonization is 26% and the percentage of classifications differing by half of a quality class is also small (16.4%). This multi-step approach to the intercalibration was endorsed by theWFD Regulatory Committee.