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The unprecedented pace of warming of the Arctic Ocean affects a wide range of pelagic processes, from primary production to fish recruitment. Sequential sediment traps deployed on oceanographic moorings at the Beaufort Sea shelf break were used to investigate the impact of variations in physical conditions on the phenology of microalgae and herbivorous copepods. Water temperature, salinity, microalgal fluxes, and zooplankton fluxes were monitored over 6 of the 7 annual cycles from September 2009 to September 2016 with a hiatus from September 2013 to August 2014. Satellite-derived sea ice concentration and snow depth were retrieved for the same period. For 5 of the 6 cycles, a consistent interval between the vernal abundance of the Calanus species (C. glacialis and C. hyperboreus), the export of the ice alga Nitzschia frigida, and peak in nauplii abundance and diatom export, reflected a match between microalgae and herbivorous copepods. Drastic changes in water temperatures and ice conditions during the 2012-2013 cycle affected this synchronization. In 2012, the record sea ice minimum extent led to anomalously high upper water temperatures during autumn and winter that led to a shoaling of the vertical distribution of C. hyperboreus females and to the production of their nauplii at shallower depths several weeks before diatom export. Due to several oceanic and atmospheric forcing, the record sea ice minimum extent was followed in 2013 by a rebound in ice cover that delayed snowmelt, sea ice melt, and ice algae export. This delay resulted in a mismatch between C. glacialis females and N. frigida fluxes and in fewer C. glacialis nauplii in June and July 2013. These mismatch events likely had a negative impact on Calanus recruitment and on the subsequent transfer of energy to carnivorous zooplankton and fish. It is crucial to maintain mooring deployments to accurately assess the wide range of effects of climate warming on the marine ecosystems.