Defining the ecosystem status of marine and estuarine waters to further assess it and implement management measures, in case of impairment, is a complex task. One of the first attempts, and most influential environmental laws, was the US Clean Water Act (CWA), which was enacted in 1948, under the name of Federal Water Pollution Control. It took its modern form in 1972, although major changes were introduced in 1977 and 1987. However, the CWA does not define the ecosystem status, but gives water quality criteria, which serves as a basis for limiting the toxicity of waste discharges to aquatic species. In addition, the biological criteria are based on the aquatic community, which describes the number (richness) and types (diversity) of species in a water body. Both could serve as a proxy of the ecosystem status. The CWA has driven the implementation of other legislation worldwide, adding new criteria to determine what can be considered as good status of waters, either fresh or marine. Hence, in Europe, the Water Framework Directive (WFD; European Commission 2000), included for the first time the concept of 'good surface water status', for continental, transitional (i.e. estuaries, lagoons) and coastal habitats (see Elliott et al. 2022 for the legislative basis of estuarine management). This means the status achieved by a surface water body when both its 'ecological status' and its 'chemical status' are at least good. In this context, 'ecological status' is an expression of the quality of the structure and functioning of aquatic ecosystems associated with surface waters. The good status is achieved when the values of the biological quality elements (i.e. phytoplankton, macroalgae, seagrasses, macroinvertebrates and fishes) show low levels of distortion resulting from human activity, but deviate only slightly from those normally associated with the surface water body type under undisturbed conditions. In turn, the 'chemical status' is based only on the achievement of the environmental quality standards for some pollutants. The major advance with the WFD was in linking the estuarine quality (Transitional and Coastal waters) to that of the catchment and treating the whole system as one. It further led to defining the estuarine water bodies as going to 'bay closing lines' (and to 1 nm from HW on the coast), thereby giving transitional waters a definition (McLusky & Elliott 2007). A few years later, the European Marine Strategy Framework Directive (MSFD; European Commission 2008) defined a new concept, related with the ecosystem-based approach (Kirkfeldt 2019), which aims at 'good environmental status'. After this Directive, the good environmental status of marine