Coastal and estuarine nurseries are composed of habitats with different biotic and abiotic features. Quantifying the contribution of different habitats within nurseries to juvenile fish feeding would help identify those that are essential in the completion of their life cycle, by providing food resources that maximise growth and survival. Essential habitats for four bentho-demersal fish species (whiting, sea bass, plaice and common sole) in an estuarine nursery were identified using gut contents and stable isotopes. Habitats differed in isotopic ratios and benthic communities. The estuarine gradient defined the macrofauna communities and sources of organic matter used by primary consumers. Trophic niche overlaps and trophic contribution of habitats highlighted that the species used both intertidal and subtidal habitats as feeding grounds. Flatfish were local feeders and fed on prey available mainly in the habitat in which they were caught, suggesting feeding behaviour that required little energy for movement. Sea bass were concentrated in upstream habitats, with intertidal mudflats contributing for nearly half of its diet. Whiting had an ubiquitous feeding strategy, suggesting that it may target prey with the most energetic gain in the habitats. Hence, habitats were used simultaneously during the same season or asynchronously throughout the year by the juvenile fish studied, suggesting no preference for a specific habitat at the community scale. Finally, both trophic tracers demonstrated the trophic importance of intertidal mudflats, especially for the sea bass and common sole, with contributions up to the half and two-third of their diet respectively.