In the Beaufort Sea, freshwater input from the Mackenzie River creates a relatively warm and turbid plume across the coastal shelf region. To determine the effects of the Mackenzie River plume on marine larval fish abundance, distribution and assemblages; this study sampled larval fish by using 500 μm bongo nets and obtaining oceanographic measurements across the plume gradient during July and August of 2007. Three larval fish assemblages were identified within three water masses: the intense plume assemblage was dominated by Pacific herring (Clupea pallasii pallasii), the diffuse plume assemblage was dominated by the sub-family Lumpeninae and the oceanic assemblage was dominated by Arctic cod (Boreogadus saida). Also, results revealed that there were no significant differences in the total larval fish abundances within these water masses. In conclusion, this study suggests that the Mackenzie River plume might be identified as an Ecologically and Biologically Significant Area (EBSA), based on the uniqueness criteria under Canada’s coastal conservation strategy.