Estuarine restoration is a major focus of coastal management. To set estuarine restoration targets, coastal managers need to understand natural baselines and human modifications. The goal of this study was to characterize baseline environmental conditions for the purposes of restoration planning at Elkhorn Slough, a regionally significant California estuary. We reconstructed baseline salinity, sediment sources, sediment accumulation rates, and wetland plant distribution by collecting and analyzing sediment cores from the upper and lower reaches of the estuary, and marsh extent by synthesizing previously published stratigraphic descriptions of sediment cores. The results of this study show strong contrasts between current and baseline conditions. Sediment accumulation rates have recently increased, whereas flood deposits have disappeared from marsh sediments. Representation by freshwater and brackish plants has also declined. Extent of marshes increased in the recent past, likely as a result of anthropogenic sediment loading from early Euro-American land use changes. Many of these marshes have degraded in past decades, but marsh extent today is still higher than in previous periods. Reconstruction of natural baselines and processes suggests that restoration strategies for the estuary should focus on increasing sediment supply and freshwater inputs to the marshes in order to restore the processes that naturally sustained marsh accretion and diversity. This study highlights the importance of revealing human modifications when designing restoration strategies for dynamic and highly altered systems such as estuaries.