Estuarine and marine ecosystems are subject to different sources of stress including changes in environmental physicochemical variables (nutrients, oxygen availability, temperature, salinity, pH) or exposure to a large cocktail of environmental pollutants. In the estuary of Bilbao, despite the improvement in environmental quality due to replacement of most polluting industries and the progressive implementation of an integrated sewage treatment plan, chronic pollution by metals and hydrocarbons still remains, together with eutrophication and pollution by emerging contaminants. The Unit of Formation and Research "Protection of Ecosystem Health" was created in 2012 through the strategic aggregation of three consolidated research groups: Cell Biology in Environmental Toxicology (CBET), Phytoplankton of estuaries and coastal areas (FITEAC) and Research on marine and estuarine pelagic environment and planktonic communities (MarEsPlank). The three groups have a long tradition in studying the health of marine and estuarine ecosystems from different perspectives, focusing in the Bay of Biscay and especially in the estuary of Bilbao. In this work we review data on the health status of the Bilbao estuary using early warning tools at the cell and tissue levels, phytoplankton assemblages and zooplankton ecology. In spite of the seasonal and interannual variability recorded for some parameters, a general recovery trend was observed for the health status in the estuary of Bilbao, with sporadic critical events such as the Prestige oil spill. (C) 2016 Elsevier Ltd. All rights reserved.