The fish community that inhabits shallow littoral areas of the Mar Menor coastal lagoon was studied seasonally. Three different habitat types were compared: deep sandy habitats, vegetated habitats and shallow muddy habitats. The results indicated that the dominant fish families in the lagoon were Mugilidae, Gobiidae, Sparidae and Atherinidae. In general, vegetated habitats and shallow muddy habitats showed higher fish abundance, biomass and fish diversity than deep sandy habitats. Moreover, fish community structure differed significantly among habitats. Vegetated habitats and shallow muddy habitats seems to play an important nursery role, mainly for marine migrant species of the Mugilidae and Sparidae families, and constituted essential habitats for species of conservationist interest such Aphanius iberus and Syngnathus abaster. Deep sandy habitats were dominated by the resident goby Pomatoschistus marmoratus. These habitat-related differences are probably related to variations in structural complexity.