Wetland managers are faced with an array of challenges when restoring ecosystems at risk from changing climate and human impacts, especially as many of these processes have been operating over decadal-millennial timescales. Variations in the level and salinity of the large crater lakes of western Victoria, as revealed over millennia by the physical, chemical and biological evidence archived in sediments, attest to extended periods of positive rainfall balance and others of rainfall deficit. The recent declines in the depth of these lakes have been attributed to a 15% decline in effective rainfall since AD 1859. Whilst some sites reveal state shifts following past droughts, the response of most wetlands to millennial-scale climatic variations is muted. Regional wetland condition has changed comprehensively, however, since European settlement, on account of extensive catchment modifications. These modifications appear to have reduced the resilience of wetlands limiting their capacity to recover from the recent 'big dry'. These sedimentary archives reveal most modern wetlands to be outside their historical range of variability. This approach provides a longer-term context when assessing wetland condition and better establishes the restoration challenge posed by the impact of climate change and variability and human impacts.