Over the centuries, land reclamation, coastal development, overfishing and pollution have nearly eliminated European wetlands, seagrass meadows, shellfish beds, biogenic reefs and other productive and diverse coastal habitats. It is estimated that every day between 1960 and 1995, a kilometre of European coastline was developed. Most countries have estimated losses of coastal wetlands and seagrasses exceeding 50% of the original area with peaks above 80% for many regions. Conspicuous declines, sometimes to virtual local disappearance of kelps and other complex macroalgae, have been observed in several countries. A few dominant threats have led to these losses over time. The greatest impacts to wetlands have consistently been land claim and coastal development. The greatest impacts to seagrasses and macroalgae are presently associated with degraded water quality while in the past there have been more effects from destructive fishing and diseases. Coastal development remains an important threat to seagrasses. For biogenic habitats, such as oyster reefs and maerls, some of the greatest impacts have been from destructive fishing and overexploitation with additional impacts of disease, particularly to native oysters. Coastal development and defence have had the greatest known impacts on soft-sediment habitats with a high likelihood that trawling has affected vast areas. The concept of ‘shifting baselines’, which has been applied mostly to the inadequate historical perspective of fishery losses, is extremely relevant for habitat loss more generally. Most habitat loss estimates refer to a relatively short time span primarily within the last century. However, in some regions, most estuarine and near-shore coastal habitats were already severely degraded or driven to virtual extinction well before 1900. Native oyster reefs were ecologically extinct by the 1950s along most European coastlines and in many bays well before that. These shellfish reefs are among the most endangered coastal habitats, but they receive some of the least protection. Nowadays less than 15% of the European coastline is considered in ‘good’ condition. Those fragments of native habitats that remain are under continued threat, and their management is not generally informed by adequate knowledge of their distribution and status. There are many policies and directives aimed at reducing and reversing these losses but their overall positive benefits have been low. Further neglecting this long history of habitat loss and transformation may ultimately compromise the successful management and future sustainability of those few fragments of native and semi-native coastal habitats that remain in Europe.