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Pacific salmon (Oncorhynchus) use a variety of rearing environments prior to seaward migration, yet large river habitats and their use have not been well defined, particularly at the southernmost salmon range where major landscape-level alterations have occurred. We explored juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) presence along the river continuum and in main-channel and off-channel habitats of a regulated California Mediterranean-climate river. Over an 8-year period, off-channels of the lower Mokelumne River exhibited slower and warmer water than the main-channel. Probability of salmonid presence varied by stream reach and habitat types. Steelhead and Chinook salmon both demonstrated transitional responses to the dry season, with juveniles leaving off-channels by midsummer. This corresponded to flow recession, increasing water temperatures, salmonid growth and end of emigration period. Main-channel steelhead observations continued until the following storm season, which brought cool flood flows to reconnect off-channels and the next juvenile cohort of both species to the river. Within arid climates, low-gradient off-channels appear more transiently used than in cooler and more northern humid climate systems. Within a highly regulated Mediterranean-climate river, off-channel habitats become increasingly scarce, disconnected or temperature limiting in low-gradient reaches both seasonally and due to anthropogenic modifications. These observations may provide guidance for future management within large salmon streams. Copyright (c) 2015 John Wiley & Sons, Ltd.