Sea-level rise during the late Pleistocene and early Holocene inundated nearshore areas in many parts of the world, producing drastic changes in local ecosystems and obscuring significant portions of the archeological record. Although global forces are at play, the effects of sea-level rise are highly localized due to variability in glacial isostatic adjustment (GIA) effects. Interpretations of coastal paleoecology and archeology require reliable estimates of ancient shorelines that account for GIA effects. Here we build on previous models for California's Northern Channel Islands, producing more accurate late Pleistocene and Holocene paleogeographic reconstructions adjusted for regional GIA variability. This region has contributed significantly to our understanding of early New World coastal foragers. Sea level that was about 80–85 m lower than present at the time of the first known human occupation brought about a landscape and ecology substantially different than today. During the late Pleistocene, large tracts of coastal lowlands were exposed, while a colder, wetter climate and fluctuating marine conditions interacted with rapidly evolving littoral environments. At the close of the Pleistocene and start of the Holocene, people in coastal California faced shrinking land, intertidal, and subtidal zones, with important implications for resource availability and distribution.