This study discusses geostrophic ocean currents and fluxes through Nares Strait, one of the major straits connecting the Arctic Ocean to the North Atlantic across the Canadian polar shelf. Between 2003 and 2006, instruments were installed on subsea moorings to measure conductivity, temperature, pressure and velocity at high temporal and spatial resolution across the 400-m-deep strait. Here we present estimates of the variable volume and liquid freshwater fluxes, derived by geostrophic calculation, through the fraction of the cross section measured by the array. The array of conductivity-temperature recorders spanned 30 km of a 38-km-wide section between 30- and 200-m depth. This domain is 48% of the total cross-sectional area, and 74% of the cross-sectional area above 200-m depth. We demonstrate the importance of the seasonal alternation between land-fast and mobile-ice conditions, which has a strong influence on the structure of the geostrophic flow and the fluxes carried by it. The three-year mean geostrophic freshwater flux through the measured domain was 20 ± 3 mSv (relative to 34.8 psu) and no less than 28 mSv if extrapolated to the surface. No significant trend over three years was detected, but the flux of freshwater through the measured domain was about 20% larger when ice was moving than when it was land-fast, with a maximum difference between individual ice seasons of 40%. Geostrophic freshwater flux in Nares Strait was forced by both wind and along-channel pressure difference during mobile-ice periods, and by along-channel pressure difference only under land-fast ice. Local winds and along-channel pressure differences explained 80% of the flux variance. Geostrophic volume flux through the measured domain was less strongly influenced by the state of the ice; its three-year mean was 0.47 ± 0.05 Sv, with a statistically significant increase of 15 ± 4% over this time. Geostrophic velocity was highly variable in space and time. The flow structure changed from a pattern with a surface jet in the center of the channel during mobile-ice conditions to another with a subsurface maximum in velocity adjacent to Ellesmere Island during fast-ice conditions. Over the three years, a second jet developed adjacent to the Ellesmere coast during mobile-ice regimes. Strong freshwater incursions synchronous with strong wind events were observed during mobile-ice seasons in the western half of the strait.