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The effects of sea level rise are now beginning to be detected in seagrass ecosystems. The present work deals with how sea level rise translates into changes on seagrass distribution at local scale and how to provide reliable information and tools to predict the vulnerability of shallow coastal ecosystems to the expected effects. To evaluate mid- and long-term changes in the habitat suitability of Zostera noltei a combination of clustering techniques—Self organizing maps and K means—considering RCP and high-end projections was used. The study, developed at the Bay of Santander, provides evidence indicating that sea level rise will highly affect meadows of Zostera noltei. This species will experience an important spatial variability, mainly in deeper areas, where moderate rising levels will substantially reduce the availability of suitable habitats for this species. This process will intensify over time and seagrass meadows are expected to be severely affected in the long term. A rising level of 0.63 m by 2100 will result in a 14.2% reduction in suitable habitats, while a 51% loss will occur with a sea level rise of 2 m. Our results indicate that large areas of seagrass in the Bay of Santander will be lost with future sea level rise, especially in the absence of major changes to sediment dynamics. However, a review of the main feedbacks and self-amplifying mechanisms regulating their adaptation allows us to be confident about Zostera noltei's capacity to adapt to changing conditions in the near future. In the long term, there are more doubts regarding this ability and possible responses remain highly uncertain. [ABSTRACT FROM AUTHOR]