Mid-ocean ballast water exchange (BWE) is recommended for international vessels to minimize the transfer of nonindigenous species (NIS). When this cannot be accomplished due to safety concerns, alternate ballast water exchange zones (ABWEZ) may be used. A coupled-ice-ocean model with meteorological forcing and particle tracking was used to evaluate the relative risks from BWE along primary shipping routes into Canada's eastern Arctic. Relative risk to receiving habitats from BWE was calculated from the product of likelihood of exposure, likelihood of establishment, and habitat sensitivity to potential NIS. Modelling results indicate that existing ABWEZs in and around Lancaster Sound and Hudson Strait are among the areas of highest relative risk for introductions of NIS via ballast water. The deeper offshore regions of Labrador Sea and Baffin Bay should be considered as alternatives. However, further research is recommended to assess the risks of NIS associated with BWE in the Canadian Arctic.