In recent years, cryoconite has received growing attention from a radioecological point of view, since several studies have shown that this material is extremely efficient in accumulating natural and anthropogenic radionuclides. The Novaya Zemlya Archipelago (Russian Arctic) hosts the second largest glacial system in the Arctic. From 1957 to 1962, numerous atmospheric nuclear explosions were conducted at Novaya Zemlya, but to date, very little is known about the radioecology of its ice cap. Analysis of radionuclides and other chemical elements in cryoconite holes on Nalli Glacier reveals the presence of two main zones at different altitudes that present different radiological features. The first zone is 130–210 m above sea level (a.s.l.), has low radioactivity, high concentrations of lithophile elements and a chalcophile content close to that of upper continental crust clarkes. The second zone (220–370 m a.s.l.) is characterized by high activity levels of radionuclides and “inversion” of geochemical behaviour with lower concentrations of lithophiles and higher chalcophiles. In the upper part of this zone (350–370 m a.s.l.), 137Cs activity reaches the record levels for Arctic cryoconite (5700–8100 Bq/kg). High levels of Sn, Sb, Bi and Ag, significantly exceeding those of upper continental crust clarkes, also appear here. We suggest that a buried layer of contaminated ice that formed during atmospheric nuclear tests serves as a local secondary source of radionuclide contamination. Its melting is responsible for the formation of this zone.