Seagrasses have declined worldwide at accelerated rates mainly due to human pressures. Moreover, climate change (e.g. sea level rise) and consequent effects, increase uncertainty about the future evolution of seagrass spatial distribution and biomass. Among other adaptive measures, habitat conservation and restoration can help to adapt and mitigate the adverse effects of climate change in marine and transitional ecosystems. In the research presented, we assess the potential future spatial distribution of Zostera noltei coverage under climate change scenarios adopting the Oka estuary (Basque Country), as a case study. For that purpose (i) a conceptual model was developed to illustrate Z. noltei system structure accounting for the environmental conditions, human activities, and climate change effects; (ii) the conceptual model was operationalised into a Bayesian network model; (iii) the main environmental variables and human activities that influence the spatial distribution of Z. noltei were identified; and (iv) suitable areas for Z. noltei considering climate change scenarios (i.e., SSP1-2.6 and SSP5-8.5) were projected. The resulting model showed a high-performance capacity (89.1\% of correctly classified instances, and 0.96 area under the curve). Depth is the main environmental variable conditioning Z. noltei coverage distribution. The future projections under climate change scenarios show that the Z. noltei area is expected to shift landward with sea level rise and that the potential gains of seagrass area will be constrained by anthropogenic barriers. The presented approach and model, demonstrate the capacity of projecting future seagrass distribution under climate change scenarios. The obtained results are a relevant source of information for management, applicable to planning and prioritisation of the most suitable areas for seagrass conservation, and the adoption of restoration actions in estuaries.