To understand how ecosystems function in ice-covered regions, we have compared two systems through extensive fieldwork with respect to productivity, key organisms on lower trophic level and vertical carbon export. In Arctic ice-covered systems, primary production and the ecosystem are constrained by the ice in different ways. The fate of the primary production, and how it is distributed between the pelagic and benthic compartment of marine ecosystems, is a key to understanding ecosystem function and energy flow. In seasonally ice-covered areas, the presence of ice cover followed by melting impact: (1) the early supply of food through ice algae; (2) the onset of primary production through light limitation to the upper water column; and (3) the annual primary production rates through meltwater induced stratification limiting nutrient supply from below. The ecosystem response to these processes is integrated in the organic material that is exported downward. Sediment trap investigations combined with studies of the pelagic system and modelling have provided insight into productivity patterns, community composition and downward export of organic material to benthos in the central and northern Barents Sea as well as on the east Greenland shelf. Different patterns emerge from open to ice-covered waters in the Barents Sea. The productive season in ice-covered waters is shorter and more intense, and is not synchronized as onset depends on local ice conditions. The annual primary production is about two times higher in Atlantic open waters, but a lower fraction of the production reaches benthos. In ice-covered waters, a lower amount of carbon but higher fraction of the total primary production reaches benthos. That suggests a less efficient pelagic community in ice-covered waters. The hydrography and ice conditions are different on the ice-covered East Greenland shelf compared with the ice-covered Barents Sea shelf. The ecosystem functions are probably also different, but so far not well known, and our knowledge only starts to emerge. During IPY and the project iAOOS Norway, we have studied this region in different seasons and the high variability in time and space induced by the sea ice and the important role of the microbial community in addition to the larger zooplankton support the picture of Arctic ecosystems being more complex and dynamic than previously thought. Their responses to a changing environment are therefore difficult to predict.