Wetland complexes in Mediterranean deltas play an important ecological role, as they harbor a diverse flora and fauna with numerous specialized species. Intensification and expansion of agricultural land use, as well as increasing withdrawal of water over the past decades, has led to considerable habitat loss in many places. Although studies from temperate Europe have already demonstrated the conservation needs of wetlands, analogous data for the Mediterranean region are very scarce. The present paper analyzes spider assemblages of the Aladjagiola wetland complex and provides ecological descriptions of diversity patterns and assemblage structures. We aim to provide the first ecological descriptions of several species and effective data sets to characterize the ecological status of the wetland habitats investigated. Spiders were collected by pitfall trapping from April to July 2008 in seven habitat types: pseudo-maquis, dry grassland (short growth), dry grassland (long growth), fringes, reed belts, humid grassland and fallow land. Diversity (alpha and functional) and evenness were both found to be lowest in humid habitat types. Community structure was analyzed by non-metric multidimensional scaling. Humid habitat types harbored a distinct species assemblage comprising many hygrophilic species that could clearly be separated from all other habitat types. By means of generalized linear models, habitat preferences of numerous xerophlic, hygrophilic and photophilic species could be assessed. Our study demonstrated that especially humid habitat types are worth protecting.