The European Water Framework Directive came into effect December 2000 in all member states. According to this directive, all European waters should reach ‘good status’ by the end of 2015. In order to assess the ecological status of their surface waters, member states have to act in concordance to a well-established step-wise plan and have to develop monitoring programs and valuation systems for a number of biological quality elements, which have been specified for each water category.This report deals with step 3 (delimitation of a reference) and step 4 (development of a score system). Subsequently, the ecological status is assessed. Assessed biological quality elements are phytoplankton, other aquatic flora, benthic invertebrates and fish. Hydromorphological status, as a supporting element for the biological quality elements, isalso assessed. Earlier studies served as a baseline to extend this research to all Flemish transitional water bodies within the Schelde basin (Van Damme et al., 2003; Brys et al., 2005) and results and insights gained from the conservations goals for the estuary where used (Adriaensen et al, 2005). While this report primarily deals with the tidal tributaries of the Zeeschelde (Flemish part of the Schelde River that has tidal regime), we tried to fill the gaps left by Brys et al. (2005), in order to obtain a comprehensive view at the entire estuary.All Flemish transitional waters have been identified as heavily modified water bodies. Therefore, maximum and good ecological potential (MEP/GEP) set the reference goals, not pristine conditions. These MEP and GEP were defined from an ecosystem perspective as an optimal functioning estuarine ecosystem. Thus, the ecological potential is conceived as the potential for natural physical, chemical and biological processes to deploy as good as possible within certain (achievable) boundaries. Attaining this potential requires an approach that surpasses the local level and individual quality elements. Therefore, an integrated, hierarchical and scale-dependent approach was chosen to establish the reference framework, including essential habitat characteristics besides the biological quality elements.At the ecosystem level, habitat area was considered, as it is a parameter relevant to all biological quality elements. Surface area of salt marsh, mudflat and shallow subtidal is also used to assess the hydromorphological status of the transitional waters. To obtain the MEP, a hydromorphological approach was used. Threshold band width was calculated as a quantifier for the space that is needed to maintain typical estuarine habitats (mudflats, salt marshes and shallow subtidal areas) in a sustainable and dynamic equilibrium of sedimentation and erosion. Along the estuary, this ‘equilibrium band width’ is proportional to the elevation range difference between the channel bottom and the mean high tide level (MHW) and the mean highest high water level (MHHW). The GEP for mudflats and salt marshes originates from the conservations goals set for the Schelde estuary: the minimum surface area of mudflat providing sufficient carrying capacity for macrobenthos, serving as (sufficient) food source for fish and birds (given good water quality). Salt marshes act as a source of dissolved silica. The minimal area of salt marshes, needed to provide sufficient amounts of silica for primary production of diatoms, is used to calculate the GEP for these marshes. The Zeeschelde and her tidal tributaries are, as a single ecosystem, in poor status, regarding the hydromorphological conditions. Dijle, Zenne, Getijdenetes and the upper Zeeschelde (Zeeschelde I) are in bad hydromorphological status. Zeeschelde II,III and Durme are also of poor status and Zeeschelde IV is in moderate status.To assess the phytoplankton of Durme and Rupel, the Flemish metric was used (Van Damme et al., 2003; Brys et al., 2005; Van Wichelen et al., 2005): chlorophyl a-concentration linked to the broader context of light climate, nutrient cycling and run-off time. The other tributaries were assessed by means of a German method (Mischke & Behrendt, 2007) comprising submetrics for phytoplankton biomass and species composition. Durme and Rupel were classified as ‘bad’, Dijle and Zenne as ‘moderate’ and the Getijdenetes as ‘good’.The macrobenthos metric consists of parameters at two scale levels:- habitat level: mudflat and shallow subtidal area- community level: application and evaluation of a number of available methods (AeTV, Dutch method, IOBS)These submetrics are subsequently integrated into a single indicator value (score). All fresh Schelde water bodies were scored ‘bad’.The macrophyte metric contains three levels:- ecosystem level: total salt marsh area- water body level: total salt marsh area and average quality of indivual marshes per water body- individual marsh level: (i) current area versus desired area (GEP) required for a sustainable development and conservation of the existing salt marshes, (ii) vegetation diversity, (iii) species richness and (iv) floristic quality index (FQI).These submetrics are subsequently integrated into a single indicator value (score), whereas the submetric values allow specific identification of bottlenecks and mitigating measures. The tributary macrophytes are scored as ‘poor’ or ‘bad’.In the fish assessment, species were selected per water body based on their discriminating power. According to their ecological demands, these species were grouped into guilds. From these guilds, relevant metrics were selected, based on their sensitivity towards anthropogenic pressures. Determination of class boundary values is based on the GEP reference list, providing the number of species per guild (metric). This number was used within each zone in order to calculate the maximum number of species and relative percentage in the total number of species for the selected guilds. Validation of the new index was based on catch data. The obtained score for the fish fauna within the studied tidal water bodies ranged from ‘bad to ‘poor’.Applying the WFD principle ‘one out, all out’, all of the 7 tidal water bodies of the Zeeschelde basin scored ‘bad’. Improvement is possible by means environmental measures which improve water and soil quality, as well as measures that provide sufficient amounts of space to the estuary, in order to allow natural functions and processes to develop naturally. Analysis of the impact of execution of the Most Desirable Alternative of the updated Sigma Plan, shows clear improvement for almost all of the considered water bodies and 3 of those 7 would rise above the GEP level boundary for the habitat area parameter.