The high abundances and cyclic distribution of remains of the freshwater fern Azolla in early-Middle Eocene sediments from the Arctic Ocean have previously been related to episodic surface-water freshening, which was speculated to be orbitally modulated. Our integrated palynological and cyclostratigraphical analysis of the recovered Azolla interval in Integrated Ocean Drilling Program (IODP) core 302-M0004A-11X resulted in the recognition of two clear periodicities: a dominant ∼1.2 m cyclicity, which we relate to changes in obliquity (∼40 k.y.), and a weaker ∼0.7 m cyclicity, which we link to precession (∼21 k.y.). Cycles in the abundances of Azolla, cysts of freshwater-tolerant dinoflagellates, and swamp-vegetation pollen show covariability in the obliquity domain. This strong correlation suggests periods of enhanced rainfall and runoff during Azolla blooms, presumably linked to increased local summer temperatures during obliquity maxima. Larix and bisaccate conifer pollen covary at the precession frequency, with peak occurrences corresponding to precession minima, possibly as a result of enhanced continental runoff from a more remote source area and a stronger seasonal contrast. Following the sudden demise of Azolla ca. 48.1 Ma, runoff (cycles) continued to influence the central Arctic at decreased intensity. This and a concomitant decline in swamp-vegetation pollen suggest edaphically drier conditions on land and decreased runoff into the Arctic Ocean, causing salinity changes, which might have been fatal for Azolla. Moreover, a sea-level rise, inferred from overall decreasing total terrestrial palynomorph concentrations, possibly facilitated oceanic connections.