While tens of millions of dollars have been spent on land acquisition and planning for current and future floodplain and wetland restoration in the Sacramento-San Joaquin Delta, knowledge of the historical processes and landscape heterogeneity that are helpful in guiding the environmental restoration are often scarce. This study used palaeoenvironmental reconstruction to increase the historical perspective, with the aim of improving environmental management. Twelve sediment cores collected from the McCormack-Williamson Tract (MWT) leveed farmland and the juxtaposed Delta Meadows (DM) tidal wetland were sampled for a suite of environmental proxies. MWT was a non-tidal flood plain during much of the late-Holocene, with a mosaic of other habitats including dry uplands, riparian forests, and freshwater wetlands persisting nearby. Comparison with the regional sea-level history suggests that the upper delta gradually came under tidal influence 3000–800 calendar years before present (cal BP). Despite this, floodplain landforms and habitats prevailed at DM from 3650–330 cal BP, after which wetlands expanded, suggesting that a flood-based disturbance regime typified the upper delta for most of the late-Holocene. Recently, the upper deltaic plain has been profoundly disturbed by agriculture and other activities, rendering significant loss of habitat. It is believed that a flood-based disturbance regime will recur at MWT if the levees surrounding the tract are intentionally breached as planned for restoration, culminating in a variety of habitats similar to pre-agricultural conditions. Concentrations of Hg, Pb, As, and P pollutants elevated several-fold in surficial sediments are of particular concern, potentially becoming problematic after restoration.