Marine species are profoundly affected by oceanographic conditions and human impacts, yet little is known about long-term historical baselines to provide context for current and future trends. This paper synthesizes >4000 years of marine ecosystem dynamics in the NW Atlantic including the late Holocene cooling and recent warming as well as Indigenous and European influence. Our multidisciplinary overview covers paleontological, archaeological, historical and modern records and future model projections. This work highlights four phases of shifting environmental and ecosystem conditions with a near-future departure from natural climate variability. These insights can help to adjust marine conservation strategies and network planning and adapt ecosystem-based management with climate change.