Numerous case studies have demonstrated that alluvial and semi-alluvial rivers in SE Australia have undergone dramatic metamorphosis in historical times. However, very few studies place these changes within a long-term evolutionary context. As a consequence, the magnitude of, and ultimate controls on, the changes to river form and processes are not fully appreciated. In this study, a paired catchment analysis is undertaken between two moderate-sized sand-bed rivers in East Gippsland, Australia. From the Thurra River, direct insight is gained into the predisturbance control exerted by riparian vegetation and wood in a lowland alluvial river. This river is effectively in the same condition today as it was at the time of the arrival of Europeans in Australia. In contrast, the adjacent Cann River, which has been settled by Europeans for 150 years, but was previously very similar to the Thurra River, exhibits stark differences today. Channel morphodynamics observed within the Thurra River, when coupled with historical and geomorphic evidence for the former condition of the Cann River, provide a detailed reference by which the recent changes to the Cann River are measured. Chronostratigraphic evidence from both flood plains places recent channel behavior within an evolutionary context extending well into the Pleistocene. Since European settlement, the study reach of the Cann River has experienced a 360% increase in channel depth, a 240% increase in channel slope, a 700% increase in channel capacity, and up to a 150-fold increase in the rate of lateral channel migration. The contemporary condition of the Cann River channel differs profoundly to that which has prevailed over at least the previous 27 ka. The first-order control on the historical channel metamorphosis is the removal of riparian vegetation and woody debris (WD). Numerous thresholds have been crossed as a result of historical channel changes, particularly the relationship between average length of woody debris pieces and channel width. Consequently, channel recovery will not simply be achieved by reintroducing the pre-existing riparian vegetation and woody debris load. Devising sound management strategies and realistic management targets for the Cann River, or any similarly altered river, requires an understanding of the long-term channel and flood plain evolutionary history, as well as the underlying controls on historical changes.