To examine the marine habitat of the endangered western stock of the Steller's sea lion (Eumetopias jubatus), two interdisciplinary research cruises (June 2001 and May to June 2002) measured water properties in the eastern and central Aleutian Passes. Unimak, Akutan, Amukta, and Seguam Passes were sampled in both years, and three additional passes (Umnak, Samalga, and Tanaga) were sampled in 2002. In the North Pacific (and to a lesser extent in the Bering Sea), a strong front in water properties was observed near Samalga Pass in June of both years, with significantly warmer, fresher, and more nitrate-poor water east of Samalga Pass than west of the pass. These water properties reflect differences in source waters (Alaska Coastal Current versus Alaskan Stream), mixing depth, and Bering Sea influence. Strong cross-Aleutian gradients were also observed with warmer, fresher water on the North Pacific side of the archipelago. The nutrient content of the waters flowing through the passes, combined with the effects of mixing within the passes, influences the transport of nutrients into the Bering Sea. As water moves away from the strong mixing of the passes and becomes more stratified, phytoplankton can take advantage of the enhanced nutrient concentrations. Thus, the northern side of the Aleutian Islands (especially in the lee of the islands) appears to be more productive. Combined with evidence of coincident changes in many ecosystem parameters near Samalga Pass, it is hypothesized that Samalga Pass forms a physical and biogeographic boundary between the eastern and central Aleutian marine ecosystems.