The ice-covered period of large Arctic rivers is shortening. To what extent will this affect biogeochemical processing of nutrients? Here we reveal, with silicon isotopes (δ30Si), a key winter pathway for nutrients under river ice. During colder winter phases in the Lena River catchment, conditions are met for frazil ice accumulation, which creates microzones. These are conducive to a lengthened reaction time for biogeochemical processes under ice. The heavier δ30Si values (3.5 ± 0.5 ‰) in river water reflect that 39 ± 11% of the Lena River discharge went through these microzones. Freezing-driven amorphous silica precipitation concomitant to increased ammonium concentration and changes in dissolved organic carbon aromaticity in Lena River water support microbially mediated processing of nutrients in the microzones. Upon warming, suppressing loci for winter intra-river nitrogen processing is likely to modify the balance between N2O production and consumption, a greenhouse gas with a large global warming potential.