The paleolimnological record of the wetlands of the Murray-Darling Basin attests to a massively elevated sedimentation rate, a shift to turbidity tolerant diatoms and the widespread loss of submerged macrophyte cover. This is understandable owing to the clearance or degradation of >70% of the original forests and woodlands, the grazing of vast stocks of sheep and cattle, but also the direct release of 400 M m3 of sediment from gold mining in Victoria alone from 1850-1880. Sediment has accumulated in wetlands owing to the increased connectivity with the River with sediment records bearing witness to rapid shallowing of billabongs and channel pools. This trajectory provides evidence to justify a diverse management response to rehabilitate functioning wetlands. The restoration of populations of small bodied fish, for example, may rely on the recovery of aquatic plant cover under improved light environments, as much as the provision of flow. Effective ecological recovery will require the identification and mitigation of the main sources of sediment. This represents a large-scale challenge over an extended planning horizon.