This study provides new constraints on the paleogeographic evolution of the Arctic during the Mesozoic. U–Pb geochronology of detrital zircon and rutile grains, together with (U–Th)/He zircon thermochronological data from the uppermost Middle Jurassic to Cretaceous strata of the Sverdrup well in the Kara Sea, reveals a major shift in sediment provenance. Two distinct age populations of detrital zircon define this transition: Group 1 (Middle Jurassic–Hauterivian) shows dominant Neoproterozoic–Cambrian (ca. 700–500 Ma) and Paleozoic (ca. 350–290 Ma) peaks, whereas Group 2 (Aptian–Albian) is characterized by prominent Paleoproterozoic (ca. 1980–1720 Ma), Paleozoic (ca. 350–255 Ma), and Early Mesozoic (ca. 240–115 Ma) ages. Corresponding variations in (U–Th)/He zircon ages—from a Triassic peak (~225 Ma) in Group 1 to a dominant Early Cretaceous peak (~140 Ma) in Group 2—support a switch from a proximal to more distal sediment source. We propose that the emergence of large continent-scale river systems transported clastic material from the southern margin of the Siberian Craton to the Arctic Ocean starting in the late Early Cretaceous. The development of a significant freshwater supply potentially initiated a thick low-salinity layer within the surface waters of the central Arctic Ocean, possibly leading to the onset of a strong salinity stratification of near-surface water masses as in the modern Arctic Ocean.