The Schelde is a lowland river originating in the northern part of France (St. Quentin), and entering the North Sea near Vlissingen, The Netherlands. The estuary covers about half of its length (355 km) as the tidal influence is stopped by sluices near Gent 160 km upstream. We focused on the Zeeschelde, the estuarine part in Flanders comprising a mesohaline, an oligohaline and a freshwater tidal zone. The Zeeschelde is subject to severe eutrophication as it receives high inputs from domestic, industrial and agricultural activities. The ecological values and nature conservation interests of the Zeeschelde are taken into consideration by a series of (inter)national policy instruments, aiming at a sustainable management and conservation of this aquatic environment. As a result several management plans apply also to the Zeeschelde or to parts of it. The most far-reaching plans are the Long Term Vision for the Schelde estuary (LTVS) and the updated Sigmaplan which combine ecological rehabilitation and sustainable habitat creation with flood control measures and navigation requisites. Compliance with almost all national and international agreements requires monitoring of biota. In the WFD fish is one of the biotic quality elements to be used in order to assess the ecological status of transitional waters. Species composition, abundance and the proportion of disturbance-sensitive species should be quantified. Any distortion attributable to anthropogenic impact is calculated by means of the Ecological Quality Ratio (EQR), representing the difference between monitored data and reference conditions. The fish-based assessment tool that we developed was designed to comply with these criteria. In addition it can be used on a metric level to assess fish species of special interest under the Habitats Directive. The fish assemblages in the Zeeschelde were described based on sampling results recorded over a period of 13 years. An overview was provided of the temporal and spatial variation in those assemblages along the salinity ...