Mismatches between ecological time and geologic time complicate our ability to effectively compare contemporary ecosystem changes with those of the past. We amassed sub-decadal paleoecological data from the California Current System (CCS) to examine how benthic ecosystem structure evolved over the past 34,000 years in the Santa Barbara Basin across the glacial-to-interglacial transition. Our results indicate that even deep-sea ecosystems of the anthropocene sensu lato - the past few centuries characterized by outsized human impacts - are distinct compared to any point in the last 34,000 years. Novel ecosystem states and heightened variability began in the early 1800s AD, suggesting that colonial-era human land-use drove the emergence of a novel ecosystem state more than a century before global climate warming began in earnest.