The shallow habitats of coastal lagoons play an invaluable role for fish communities as nursery areas and provide essential habitats for threatened fish species. Shoreline modification is an anthropogenic coastal stressor that can negatively affect aquatic communities through the modification of nearshore habitats. The aim of the present study was to quantify the effects of two types of shoreline conditions on habitat structure and fish community of littoral habitats. Unmodified shorelines adjacent to saltmarshes and recreational beaches in urbanised areas of the Mar Menor coastal lagoon were compared. The results showed that there were significant differences in habitat structure, fish community structure and fish species abundance by shoreline type. Recreational beaches were characterised by higher water depth and homogeneous substrata, while unmodified shorelines showed high substrata heterogeneity and supported well developed meadows of submerged vegetation. The latter shoreline type provided an important nursery habitat for marine species such as Sparus aurata and Liza saliens, and represented critical habitats for species of conservation concern such as Aphanius iberus and Syngnathus abaster. Littoral areas adjacent to modified shorelines were dominated by Pomatoschistus marmoratus. We suggest that urbanisation has impacted fish assemblages through degradation of habitat structure (loss of complexity and refuge areas).