1. Within a few decades of European disturbance in the mid-nineteenth century, river character and behaviour were transformed in Bega catchment on the south coast of New South Wales, Australia. Ecological impacts of geomorphic changes to river structure and function throughout the catchment are assessed. 2. At the time of European settlement, many water courses in Bega catchment were discontinuous, with extensive swamps along middle and upper courses. Following a series of direct and indirect human impacts, channels became continuous in the middle and upper parts of the catchment, as extensive valley fills at the base of the escarpment were incised. Along the lowland plain, the channel widened by over 300%, fundamentally altering the relationship between the channel and its adjacent floodplain. 3. Geomorphic changes to river structure have modified habitat availability throughout Bega catchment. The impacts have been least pronounced in headwater streams, but have been dramatic along virtually all river courses beyond the base of the escarpment. 4. Changes in river structure have been directly related to altered riparian vegetation cover, and vice versa. As a consequence of changes to river structure, bed substrate calibre (and supply volume/rate) has been modified along most streams. 5. A series of indirect, secondary impacts have modified habitat viability along river courses. Lateral, longitudinal and vertical linkages within the river system have been altered, affecting the transfer of water, sediment, organic matter, nutrients and other biotic interactions. 6. These direct and indirect consequences of geomorphic changes in river structure suggest that ecologists need to adopt a longer-term, catchment-framed view of human disturbance to river ecosystems. 7. Effective, sustainable ecological rehabilitation of river courses is dependent on an understanding of geomorphic processes and determination of appropriate river structure at differing positions in catchments.