<p>Wetlands are decreasing globally and species that depend on these habitats must adjust their behaviour or may face population declines. Protected wetlands designed for the conservation of certain species may fail to meet their objectives if habitats critical for specific behaviours are degraded, even if other habitats remain unaffected. It is therefore important to better understand the functional role of specific coastal wetland habitats and when species need them. We investigated the behaviour of juvenile spoonbills (<i>Platalea leucorodia</i>) from two Portuguese protected wetlands: the Tagus estuary and Ria Formosa coastal lagoon. Forty-four juvenile spoonbills were equipped with GPS/GSM tags with a 3-axial accelerometer, which allowed integrating spatially explicit behaviour with land use data. We then explored how habitat use changes with diel and tidal cycles within these dynamic landscapes and assessed the functional role of habitats. Juvenile spoonbills vary their daily routines according to the composition of habitats in their natal wetland, with the diel cycle being more influential in the Tagus estuary, while in Ria Formosa both cycles (diel and tidal) were of similar relevance. Habitats were used differently within the study areas: intertidal flats accounted for 62.09% of feeding activity in Ria Formosa versus 47.16% in the Tagus estuary, where rice fields represented the highest feeding percentage (52.27%). This work highlights the need for species- and site-specific studies and can serve as a template for understanding habitat use by other species (or different life stages) to support the development of targeted conservation measures.</p>