Little is known about the dynamics of marine food chains spanning primary to higher trophic levels on centennial and longer timescales, especially where the supply of dissolved iron limits primary productivity. To elucidate the long-term dynamics of biological productivity in the Coastal Oyashio (CO), which is a major pathway for transporting dissolved iron into the western North Pacific from winter to spring, we reconstructed the lower trophic level productivity over the last 3000 years in the CO. Our results demonstrate that the concentrations and mass accumulation rates of both Chl-a (chlorophyll a and its derivatives) and biogenic opal used as proxies of primary productivity, and steryl chlorin esters (SCEs) used as that of zooplankton productivity, show a millennial-scale increasing trend and centennial-scale variability beginning ca. AD 400. SCEs were positively correlated with Chl-a, indicating that changes in zooplankton productivity were induced by bottom-up control of primary productivity. The Chl-a and SCEs showed synchronous centennial-scale patterns with a relative abundance of sea-ice-associated diatom species transported by CO, and with a ventilation index in the Okhotsk Sea Intermediate Water. This synchronous pattern indicates that lower trophic-level productivity during the spring bloom responded to the intensity of iron-replete CO.