Wetlands are among the most endangered ecosystems worldwide with multiple direct and indirect stressors, especially in human-altered areas like intensive agricultural landscapes. Conservation management and efforts often focus on species diversity and charismatic taxa, but scarcely consider habitats. By focusing on a complex formed by 107 permanent wetlands at 18 Natura 2000 sites in the Emilia-Romagna region (northern Italy), the patterns of habitats of conservation concern were investigated and the concordance with threatened species patterns was analysed. Wetlands were characterised in terms of morphology, connectivity, land use and management as drivers of assemblage and richness patterns of habitats. Our results showed a strong concordance between the distribution and richness patterns of both habitats and threatened taxa (birds, mammals, amphibians, reptiles, fish, invertebrates, and plants). Thus, habitats seem an effective proxy of species patterns. The variables related with perimeter, environmental heterogeneity and presence of water bodies were the most important ones associated with habitat richness patterns. The presence of aquatic systems (measured as the percentage of wetland area occupied by an aquatic surface) and their position in the hydrographic network were associated mostly with habitats distribution. Low richness wetlands (in habitat terms) were not complementary as no new habitat types were supported. The results stressed the relevance of wetlands with wide water body perimeters composed of diverse systems as being key for biodiversity conservation in a simplified agricultural matrix. Integrating habitat- and species-based perspectives seems a promising field and may provide a rapid assessment tool to acquire effective information for wetlands conservation and assessment.