Determining hydrologic conditions prior to instrumental records is a challenge for restoration of freshwater ecosystems worldwide. Paleoecologic data provide this information on past conditions and when these data are used to adjust hydrologic models, allow conditions to be hindcast that may not be directly estimated from the paleo-data alone. In this context, the paleo-data provide real-world estimates as input to the models. Restoration of the Greater Everglades Ecosystem requires this understanding of the hydrology of the natural system prior to significant alterations due to water management and land use. Large scale models such as the Natural Systems Model (NSM 4.6.2) have been used by the South Florida Water Management District and other agencies responsible for restoration to estimate past hydrologic conditions; however, these models typically portray a drier natural system for the beginning of the 20th century than what is indicated by paleoecologic analyses and historical data. The purpose of this study is to estimate pre-20th century water levels, hydroperiods and flow in the freshwater wetlands of the Everglades by using pollen assemblage data in three sediment cores to adjust the Natural Systems Model. This study is designed to further test estimates of flow through the Everglades derived from analysis of sediment cores collected in Florida Bay. The results demonstrate that the NSM 4.6.2 underestimates water levels and hydroperiods in the Everglades compared to the paleo-adjusted NSM 4.6.2 model outputs. Flow models that use the paleo-adjusted water levels as input indicate flow through Shark River Slough in the late 19th century was approximately two times flow between 1990 and 2000, and flow through Taylor Slough was approximately three times flow between 1990 and 2000. The flow estimates derived from this study agree with the estimates derived from earlier studies using estuarine cores. This integration of paleoecologic information and hydrologic models provides resource managers with the best available estimates of past conditions and allows them to set realistic targets for restoration of freshwater ecosystems.