Flood-induced renaturalization of the Becva River segments was studied applying multidisciplinary approach. Ecological linkages among channel units and stream biota (macroinvertebrates, algae, fish) were identified. Specific macroinvertebrate taxa and community characteristics were found for four types of river habitats (channel units). Based on a position in the channel and using hydraulic thresholds a distinction was made among riffles and pools in central part of the main channel, marginal zone of the main channel and lateral arms/pools. Differentiation of stream biota between central-channel and lateral habitats was related to the degree of their isolation (connectivity of side arms). Partial recovery of channel forming processes, increased bank zone heterogeneity, temporal occurrence of large woody debris in the channel and formation of lateral channels/pools characterized renaturalization process of the Becva River at the studied segments.