In fluvial systems, the interactions between rivers and groundwater significantly affect various ecological structures (for example, riparian vegetation) and functions. To examine the effects of hydrological exchange between groundwater and surface water on the distribution of aquatic invertebrates within a riverine landscape, we investigated the main stem, tributaries, and various surface and subsurface waters of two floodplains of a southern Alpine river (Brenno, Switzerland) in terms of their physicochemical, hydraulic, substratum, and faunal characteristics. The origins of the water were investigated by analyzing geomorphic settings and physicochemical variables. The two floodplains had different hydrological regimes. The middle floodplain was dominated by lateral inputs and exfiltration of hillslope groundwater from two different subcatchments. Bank filtration of river water sustained subsurface water only close to the channel. The aquatic habitats of the middle floodplain formed a rather homogeneous group with high taxon richness and intrahabitat diversities. These aquatic habitats resembled mountain springbrooks in their physicochemical characteristics and faunal compositions. In the lower floodplain, the exchange between river water and groundwater was more extensive. The aquatic floodplain habitats of the lower floodplain were fed mainly by deep and shallow alluvial groundwater, hyporheic exfiltration, and partly by surface water. In contrast to aquatic habitats of the middle floodplain, habitats of the lower floodplain showed a low intrahabitat and a high interhabitat diversity in terms of both substrate characteristics and faunal compositions. For both floodplains, ordination analyses showed a high concordance between the structure of the invertebrate community and the characteristics of the environmental habitat, including chemical, geomorphic, and hydraulic variables. Ordinations grouped aquatic habitats according to the origins of the waters. Taxon richness was related to local structural diversity, but species turnover was related to differential vertical and lateral connectivity. Exfiltration of groundwaters provided aquatic floodplain habitats for several specialized species. The results of this study show the significance of the river-groundwater connectivity for the creation of the habitat mosaic that sustains biodiversity in floodplains and thus have important implications for managing the ecological integrity of floodplains.