Fish-based indices monitor changes in surface waters and are a valuable aid in communication by summarising complex information about the environment (Harrison and Whitfield, 2004). A zone-specific fish-based multimetric estuarine index of biotic integrity (Z-EBI) was developed based on a 13 year time series of fish surveys from the Zeeschelde estuary (Belgium). Sites were pre-classified using indicators of anthropogenic impact. Metrics showing a monotone response with pressure classes were selected for further analysis. Thresholds for the good ecological potential (GEP) were defined from references. A modified trisection was applied for the other thresholds. The Z-EBI is defined by the average of the metric scores calculated over a one year period and translated into an ecological quality ratio (EQR). The indices integrate structural and functional qualities of the estuarine fish communities. The Z-EBI performances were successfully validated for habitat degradation in the various habitat zones.