Spatial modelling is an emerging approach to the management of coastal marine habitats, as it helps understanding and predicting the results of global change. This paper reviews critically two recent examples developed in Liguria, an administrative region of NW Italy. The first example, aiming at predicting habitat status depending on pressures, provides managers with the opportunity of envisaging different scenarios for the consequences of coastal development choices. The second example defines the status of an important Mediterranean coastal marine habitat (Posidonia oceanica meadows) under natural conditions, allowing for quantifying human impacts on regressed meadows. Both modelling approaches are useful to define the targets of coastal management, and may help choosing the best management option. Well-planned and sustained monitoring is essential to model validation and improvement.