The Minho River estuary is located in the western Iberian margin (SW Europe), in the border region between the Minho (north of Portugal) and Galicia (Spain) regions. It is classified as a mesotidal estuary, covering a total area of 23 km2. The estuary has a great socio-economic importance, providing goods and services to about 80,000 of persons. It has also a high ecological value, mainly due to its large diversity of habitats and biodiversity (it is included in NATURA 2000; it is classified as a “Zona de Protecção Especial para Aves” (ZEP), an “Important Bird Area” (IBA) and is a CORINE Biotope). The high productivity of this estuary makes it a refuge place for nursery and feeding of marine species, essential to ecosystem functioning. The Minho estuary is still relatively low impacted by anthropogenic activities, however, in the last decades, the environmental pressures and impacts have been increasing, with the most important at the present being: physical and hydrological alterations mainly due to the construction of dams and other facilities to support human activities (e.g. fluvial transport of people and goods, touristic activities, etc); the presence of non-native (exotic) invasive species that have been contributed to the decline of several native species, including some with high economic and conservational interest; and organic and chemical contamination produced or increased by anthropogenic activities (industrial, urban and agricultural sources) still found in low concentrations in water, sediments and organisms but with a general increasing trend over the years; and alterations resulting from global climate changes. This ecosystem has been intensively studied, especially in the last two decades, in relation to hydromorphological characteristics, water quality, communities diversity and functioning, populations health, pollution, among other aspects. However, more knowledge is still needed on environmental chemical contamination and on the effects of complex mixtures of those pollutants in wild populations, communities and ecosystem functioning. In addition, more attention should be given to alterations resulting from global climate changes, in particular in relation to extreme events (e.g. heat waves, floods) and interactions between pollution, invasive species, and abiotic factors variation. Knowledge on plants and microorganisms (especially pathogens and parasits) is lacking.