Embracing spatial heterogeneity is seen as a next frontier for ecosystem ecology. Ecosystems need to be considered as interacting mosaics rather than homogeneous entities, and the composition and the spatial configuration of patches, as well as the boundary properties (e.g. permeability), need to be used as variables for predicting biodiversity and ecosystem processes. Floodplains are ideal model ecosystems to study (i) the processes that create and maintain environmental heterogeneity and (ii) to quantify its effects on ecosystem functioning and biodiversity. For example, flow and flood pulses create a shifting mosaic of interconnected aquatic and terrestrial habitat patches. Composition and spatial arrangement of these habitat patches controls the flux of organisms and matter among adjacent patches, and the capacity of a habitat to process matter dependents on the productivity of adjacent patches and on the exchange among these patches. The exchange of matter and organisms among habitats of different age and productivity is often pulsed in nature. Small pulses of a physical driver (e.g. short-term increase in flow) can cause mass emergence of aquatic insects and therefore impact recipient terrestrial community structure. Today, the active conversion of simplified ecosystems back to a more heterogeneous state has become an important aspect of restoration and management.