Iron (Fe) availability impacts marine primary productivity, influencing the efficiency of the biological pump. Stable Fe isotope analysis has emerged as a tool to understand how Fe is sourced and cycled in the water column. However, distinguishing the major Fe sources in sediment records based on their Fe isotope compositions alone is challenging as sources can exhibit overlapping values. To address this issue, we studied three pelagic clay sequences spanning the past 90 million years. First, we used osmium isotope chronostratigraphy to date the sequences. Second, we analyzed leachates of the sediments for their multi-element concentration and Fe isotope compositions. Third, we used statistical modeling to reveal five principal Fe sources to the sites—dust, distal background, two hydrothermal fluids, and a magnesium-rich volcanic ash—which share similar depositional histories. Initially, hydrothermal inputs dominated Fe deposition, shifting to increased contributions from other sources as the sites migrated away from their respective mid-ocean ridges. Notably, between 66–40 Ma, distal background sources became significant, before the sites shifted to increasing dust dominance around 30 million years ago. Our analysis suggests that the modern South Pacific is the most dust-dominated it has been in ≈90 million years, which is significant considering the low rates of dust deposition to this region. Our approach establishes a framework combining isotope measurements, geochemical analysis, and statistical modeling to explore the history of Fe delivery to the ocean. This approach holds potential for understanding the interplay between Fe delivery, the biological pump, and Earth’s climate across geological timescales.