Climate extremes that cause droughts, floods, or large temperature fluctuations can complicate ecosystem restoration efforts focused on local and regional human disturbance. Restoration targets are often based primarily on monitoring data and modeling simulations, which provide information on species' short-term response to disturbance and environmental variables. Consequently, the targets may be unsustainable under the spectrum of natural variability inherent in the system or under future climate change. Increasingly, ecologists and restoration planners recognize the value of the long temporal perspective provided by paleoecological data. Advances in paleoclimatology, including better climate proxy methods and temporal resolution, contribute to our understanding of ecosystem response to anthropogenic and climatic forcing at all time scales. We highlight paleoecological research in the Chesapeake Bay and the Florida Everglades and summarize the resulting contributions to restoration planning. Integration of paleoecological, historic, monitoring, and modeling efforts will lead to the development of sustainable, adaptive management strategies for ecosystem restoration.