Juvenile Pacific salmon (Oncorhynchus spp.), ecologically-related species, and associated biophysical data were collected along primary marine migration corridors in the northern and southern regions of southeastern Alaska in 2006. Up to 21 stations were sampled over four time periods (39 sampling days) from May to August. This survey marks 10 consecutive years of systematic monitoring on how juvenile salmon interact in marine ecosystems, and was implemented to identify the relationships among biophysical parameters that influence the habitat use, marine growth, predation, stock interactions, and year-class strength of salmon. Typically, at each station, fish, zooplankton, surface water samples, and physical profile data were collected using a surface rope trawl, conical and bongo nets, water sampler, and a conductivity-temperature-depth profiler during daylight. Surface (3-m) temperatures and salinities ranged from 7.1 to 15.4 ºC and 15.1 to 32.0 PSU from May to August. A total of 10,641 fish and squid, representing 20 taxa, were captured in 94 rope trawl hauls from June to August. Juvenile salmon comprised about 98% of the total fish and squid catch in each region. Juvenile salmon occurred frequently in the trawl hauls, with pink (O. gorbuscha), chum (O. keta), sockeye (O. nerka), and coho salmon (O. kisutch) occurring in 52100% of the trawls in both regions, whereas, juvenile Chinook salmon (O. tshawytscha) occurred in 25% and 28% of the hauls in the southern and northern regions. Of the 10,451 salmonids caught, over 99% were juveniles. In both regions, only two non-salmonid species represented catches of >27 individuals: walleye pollock (Theragra chalcogramma) in the southern region and Pacific herring (Clupea pallasi) in the northern region. Temporal and spatial differences were observed in the catch rates, size, condition, and stock of origin of juvenile salmon species. Catch rates of juvenile salmon in both regions were generally highest in June for all species except Chinook, which had the highest catch rates in July. Size of juvenile salmon increased from June and July; mean fork lengths were: 102 and 121 mm for pink; 112 and 138 mm for chum; 110 and 131 mm for sockeye; 168 and 200 mm for coho; and 202 and 223 mm for Chinook salmon. Coded-wire tags were recovered from 13 juvenile coho salmon, two juvenile and one immature Chinook salmon; all but two were from hatchery and wild stocks of southeastern Alaska origin. The non-Alaska stocks were juvenile Chinook salmon originating from the Similkameen River and the Wells Hatchery within the Columbia River Basin. Alaska enhanced stocks were also identified by thermal otolith marks from 77% of the chum and 7% of the sockeye salmon. Onboard stomach analysis of 95 potential predators, representing 12 species, revealed one predation incident on juvenile salmon by an adult coho salmon. This research suggests that in southeastern Alaska, juvenile salmon exhibit seasonal patterns of habitat use and display species- and stock-dependent migration patterns. Long-term monitoring of key stocks of juvenile salmon, on both intra- and interannual bases, will enable researchers to understand how growth, abundance, and ecological interactions affect year-class strength and to better understand the role salmon play in North Pacific marine ecosystems.