The diel vertical migration (DVM) of zooplankton is one of the largest species migrations to occur globally and is a key driver of regional ecosystems. Here, time series of acoustic data collected at the circumpolar Arctic polynya system were used to examine the annual cycle of DVM. We revealed that the formation of polynya open water disrupts DVM. This disruption is attributed to a predator avoidance behavior of zooplankton in response to higher polar cod abundance attracted by the polynya.