Large-scale ecosystem restoration projects seldom undergo comprehensive evaluation to determine project effectiveness. Consequently, there are missed opportunities for learning and strategy refinement. Before our study, monitoring information from California’s middle Sacramento River had not been synthesized, despite restoration having been ongoing since 1989. Our assessment was based on the development and application of 36 quantitative ecological indicators. These indicators were used to characterize the status of terrestrial and floodplain resources (e.g., flora and fauna), channel dynamics (e.g., planform, geomorphology), and the flow regime. Indicators were also associated with specific goal statements of the CALFED Ecosystem Restoration Program. A collective weight of evidence approach was used to assess restoration success. Our synthesis demonstrates good progress in the restoration of riparian habitats, birds and other wildlife, but not in restoration of streamflows and geomorphic processes. For example, from 1999 to 2007, there was a > 600% increase in forest patch core size, and a 43% increase in the area of the river bordered by natural habitat > 500 m wide. Species richness of landbirds and beetles increased at restoration sites, as did detections of bats. However, degraded post-Shasta Dam streamflow conditions continued. Relative to pre-dam conditions, the average number of years that pass between flows that are sufficient to mobilize the bed, and those that are of sufficient magnitude to inundate the floodplain, increased by over 100%. Trends in geomorphic processes were strongly negative, with increases in the amount of bank hardened with riprap, and decreases in the area of floodplain reworked. Overall the channel simplified, becoming less sinuous with reduced overall channel length. Our progress assessment presents a compelling case for what needs to be done to further advance the ecological restoration of the river. The most important actions to be taken relate to promoting river meander and floodplain connectivity, and restoring components of the natural flow regime.