This compilation of new information and summaries of earlier work emphasizes variability within marine waters of the Aleutian Archipelago. From the Alaska Peninsula to Near Strait, net flow through the passes is northward, with four passes (Amukta, Amchitka, Buldir, and Near Strait) contributing most of the flow. East of Samalga Pass (169°W), waters derived from the Alaska Coastal Current predominate, whereas west of Samalga Pass, waters of the Alaskan Stream predominate. The pattern of storm tracks creates a climatological (interannual and long term) transition zone in weather features (e.g. surface air temperature) near 170°W. The marine ecosystem of the Aleutian Archipelago also has a strong discontinuity at Samalga Pass, where cold-water corals, zooplankton, fish, marine mammals and foraging seabirds show a step change in species composition. Diets of ground fish, Steller sea lions (Eumetopias jubatus) and some seabirds also change there. Lower growth rates of some fish species and stable isotope data indicate that productivity declines westward along the archipelago. The available data demonstrate considerable ecosystem variability over time scales of decades to millennia. Abrupt changes in composition of fish communities at several of the major passes suggest that Samalga Pass may mark only one of several ecological divisions of Aleutian waters. This spatial and temporal heterogeneity provides an important context within which to view recent declines in populations of Steller sea lions and other species, and has important implications for the management of regional marine resources. We conclude that the marine waters of the Aleutian Archipelago are divided into at least two different ecological regions, with potential for a concomitant separation of some fishery resources.