Fish-based indices monitor changes in surface waters and are a valuable aid in communication by summarisingcomplex information about the environment (Harrison and Whitfield, 2004). A zone-specificfish-based multimetric estuarine index of biotic integrity (Z-EBI) was developed based on a 13 year timeseries of fish surveys from the Zeeschelde estuary (Belgium). Sites were pre-classified using indicators ofanthropogenic impact. Metrics showing a monotone response with pressure classes were selected for furtheranalysis. Thresholds for the good ecological potential (GEP) were defined from references. A modifiedtrisection was applied for the other thresholds. The Z-EBI is defined by the average of the metric scorescalculated over a one year period and translated into an ecological quality ratio (EQR). The indices integratestructural and functional qualities of the estuarine fish communities. The Z-EBI performances weresuccessfully validated for habitat degradation in the various habitat zones. ; JRC.H.1 - Water Resources