Restoration of the Kissimmee River and floodplain ultimately will involve restoring 70 km of river channel and riparian zone and 11,000 ha of wetland over a period of two decades. Restoring ecosystem integrity is a crucial goal of the project, and the evaluation program is designed to assess the success of this endeavor. Major components of the riverine and floodplain ecosystem will be evaluated, guided by conceptual models of their structure and function. These studies will be referenced to historic conditions of the past and to present-day conditions in the channelized system. Enhanced connectivity and interactions between the river and floodplain, the interplay of abiotic and biotic variables, and interactions between trophic levels will restructure the channelized river and the largely drained floodplain that now exist. The key to evaluating the success of this ambitious project will be selecting measurements of the structure and function of the river and floodplain ecosystems that are responsive to this large-scale manipulation. The timing and duration of floodplain inundation, improved dissolved oxygen conditions, germination and establishment of wetland vegetation, and enhancement and expansion of rheophilic benthic invertebrate populations are critical initial elements of restoration. Further expected outcomes are an increase in the primary productivity of the ecosystem, expansion of the fish community into the reopened channels and onto the reflooded floodplain, and improved visitation and use by waterbirds in the restored regions. We highlight predictions of some of these key linkages and primary structural and functional attributes of the restored river and floodplain that should be measured.