We provide an overview of the physical oceanographic and geological processes that affect marine biological habitats and production in the marine waters throughout the archipelago and continental shelf of Southeast Alaska. Given the paucity of regional data, our overview summarizes work done in adjacent regions of the Gulf of Alaska shelf and basin, and draws on research carried out in similar settings elsewhere. The geological setting, which critically influences the regional meteorology and oceanography, includes a narrow continental shelf, deep channels that permeate the archipelago, fjords, glaciers and a rugged, mountainous coast. The large-scale meteorology is influenced primarily by seasonal variations in the intensity and position of the Aleutian Low. Winds, freshwater runoff, tides and cross-shelf exchange control the regional oceanography. The large-scale flow field advects mass, heat, salt, nutrients and planktonic organisms northward from British Columbia (and even further south) to the northern Gulf of Alaska along the slope, shelf, and within the channels of Southeast Alaska. The deep channels permeating the island archipelago and narrow continental shelf facilitate communication between basin and interior waters. Water properties and flow fields are subject to large annual variations in response to similarly large variations in winds and coastal freshwater discharge. The complex geological setting leads to large spatial heterogeneity in the physical processes controlling the local circulation fields and mixing, thereby creating numerous and diverse marine biological habitats. These various circulation and mixing processes modify substantially Southeast Alaska water masses and thus influence marine ecosystem processes downstream over the northern and western Gulf of Alaska shelf.