This study examined the 1979–2004 volume and freshwater fluxes through the Canadian Arctic Archipelago (CAA) and into the Labrador Sea using a high resolution (∼9 km) coupled ice-ocean model of the pan-Arctic region to provide a reference, compare with limited observational estimates, and investigate control mechanisms of this exchange. The 26-year mean volume and freshwater fluxes through Nares Strait were 0.77 Sv ± 0.17 Sv and 10.38 mSv ± 1.67 mSv respectively, while those through Lancaster Sound amounted to 0.76 Sv ± 0.12 Sv and 48.45 mSv ± 7.83 mSv respectively. The 26-year mean volume and freshwater fluxes through Davis Strait were 1.55 Sv ± 0.29 Sv and 62.66 mSv ± 11.67 mSv while the modeled Fram Strait branch provided very little (∼2%) freshwater into the Labrador Sea compared to the total CAA input. Compared to available observations, the model provides reasonable volume and freshwater fluxes, as well as sea ice thickness and concentration in the CAA. In Nares Strait and Lancaster Sound, volume flux anomalies were controlled by the sea surface height (SSH) gradient anomalies along the straits and freshwater anomalies were highly correlated with the volume anomalies. At least half of the variance in the time series of SSH gradient anomaly was due to SSH anomalies in northern Baffin Bay. The West Greenland Current (WGC) exhibits seasonality, with cross shelf flow (into the Labrador Sea) peaking in January/February/March, while reducing the northward flow across eastern Davis Strait. We hypothesize that the eddy-reduced northward flow of WGC results in the lower volume and SSH in Baffin Bay. This maximizes the SSH gradients between the Arctic Ocean and Baffin Bay, leading to maximum winter volume fluxes through Nares Strait and Lancaster Sound. Model limitations include the insufficient spatial resolution of atmospheric forcing (especially to account for the effects of local topography), the representation of river runoff into Hudson Bay and coastal buoyancy currents, low mobility of modeled ice, and incomplete depiction of ice arching. Many of these issues are expected to be resolved with increased model grid cell resolution, improved sea ice and ocean models and more realistic atmospheric forcing.