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Abstract A major challenge in ecology is to link patterns and processes across different spatial and temporal scales. Flood plains are ideal model ecosystems to study (i) the processes that create and maintain environmental heterogeneity and (ii) to quantify the effects of environmental heterogeneity on ecosystem functioning and biodiversity. Fluvial processes of cut‐and‐fill alluviation create new channels, bars and benches within a flood plain that in turn provides new surface for subsequent vegetative recruitment and growth resulting in a shifting mosaic of interconnected aquatic and terrestrial habitat patches. Composition and spatial arrangement of these habitat patches control the movement of organisms and matter among adjacent patches; and the capacity of a habitat to process matter depends 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 leach large amounts of nutrients thereby stimulating primary production in adjacent aquatic patches, or trigger mass emergence of aquatic insects that may in turn impact recipient terrestrial communities. Hence, biodiversity in a river corridor context is hierarchically structured and strongly linked to the dynamic biophysical processes and feedback mechanisms that drive these chronosequences over broad time and space scales. Today, the active conversion of degraded ecosystems back to a more heterogeneous and dynamic state has become an important aspect of restoration and management where maintaining or allowing a return to the shifting habitat mosaic dynamism is the goal with the expected outcome greater biodiversity and clean water among other valuable ecosystem goods and services. Copyright © 2009 John Wiley & Sons, Ltd.