The seasonal mixing within Ellis Fjord and its relationship to the ocean are described using temperature, salinity and freshwater input data. The fjord is ice covered for 11–12 months of the year, is up to 117 m deep and has six major basins, two of which at its head are meromictic (in which some water remains partly or wholly unmixed with the main water mass at the circulation periods), hypersaline and permanently anoxic.

There was a restricted water exchange during the winter and early spring between the fjord and the ocean, with the vertical mixing dominated by brine convection from salt released by the thickening ice sheet. This convection destroyed both the early winter stratification in the oxic basins and the isopycnal waters linking the sills of the meromictic basins to the deeper waters of the downstream oxic basins. Brine convection also produced waters of elevated salinity, in the shallows of all the basins, which gravitated as density currents to the bottoms of their respective basins. This process was responsible for producing hypersaline conditions at the bottoms of the two meromictic basins during the mid-holocene period. Brine continued to drain from the ice in early spring but without an increase in ice thickness. This served to convect surface waters, recently warmed through solar radiation, throughout the water columns of the oxic basins.

Stratification of the surface waters, over summer, was greater in the landward basins than in the seaward basins. This may have been a result of a buoyant tidal jet emanating from the mouth of the fjord, destroying stratification in the seaward basins. As a result, warmer water of lower salinity from the basin outside the fjord had mixed down to the bottom of the first basin during late spring and summer.