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Abstract: A three dimensional coupled ocean (HYCOM) and sea ice model (CICE) is applied to a regional setup of the Lincoln Sea, the Nares Strait, and the Baffin Bay. As the sea ice model is originally developed for global simulations, boundary conditions have been implemented for the regional setup. The model results are compared with satellite images and with the large scale simulation that is specified for the boundary conditions. The main focus in this paper is on the simulated variations in the modeled sea ice flux and oceanic volume flux through the Nares Strait in the period September 2005–August 2008. The total sea ice area flux in 2006 is 14×103 km2/year and in 2007 it is 69×103 km2/year. The reason for this difference is mainly the blocking of the ice flow in the Nares Strait in spring 2006. The corresponding volume fluxes are 20km3/year and 120km3/year. The average annual oceanic volume flux varies from 0.6Sv to 1.3Sv from 2006 to 2008. The freshwater flux with a reference salinity of 34.8 varies in the same period from 12mSv to 29mSv. The opening and closing of the North Water, which is one of the largest polynyas in the world, are investigated. A February storm event with opening and refreezing of the North Water is well reproduced. The model results show that the net heat flux in the polynya area at the surface is positive into the ocean from May until the end of July, and hence while the wind is responsible for opening the polynya, the main mechanism for maintaining the polynya in late spring and early summer is the surface heat flux. [ABSTRACT FROM AUTHOR]