Juvenile Pacific salmon (Oncorhynchus spp.), ecologically-related species, and associated biophysical data were collected by the Southeast Coastal Monitoring Project along primary marine migration corridors in the southern and northern regions of southeastern Alaska. Up to 17 stations were sampled in four time periods (40 sampling days) from May to August 2005. This survey marked the ninth consecutive year of systematic monitoring of 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, physical profile data, and water samples were collected using a surface rope trawl, conical and bongo nets, a conductivity-temperature-depth profiler, and a water sampler during daylight. Surface (3-m) temperatures and salinities ranged from 9.3 to 15.7 ºC and 13.8 to 31.5 PSU over the season. A total of 6,874 fish and squid, representing 19 taxa, were captured in 92 rope trawl hauls from June to August. Juvenile salmon comprised 96% of the total fish and squid catch in each region. Juvenile salmon occurred frequently in both regions, with pink (O. gorbuscha), chum (O. keta), sockeye (O. nerka), and coho (O. kisutch) occurring in 63-86% of the trawl hauls, and juvenile Chinook salmon occurring in 20-25% of the trawl hauls. Of the 6,651 salmonids caught, over 99% were juveniles. In both regions, only two non-salmonid species represented >1% of the catch: market squid (Loligo spp.) in the southern region (2%) and crested sculpin (Blepsias bilobus) in the northern region (2%). 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 were highest in June for all species except pink salmon, which had the highest catch rates in August. Size of juvenile salmon increased steadily throughout the season; mean fork lengths in June, July, and August were, respectively: 92, 127, and 170 mm for pink; 108, 124, and 191 mm for chum; 115, 123, and 180 mm for sockeye; 184, 207, and 239 mm for coho; and 205, 245, and 255 for Chinook salmon. Coded-wire tags were recovered from 17 juvenile coho, 6 juvenile Chinook, and 2 immature Chinook salmon; all but six of these fish were from hatchery and wild stocks of southeastern Alaska origin. The non-Alaska stocks were juvenile coho and Chinook salmon originating from Oregon and Washington. Alaska enhanced stocks were also identified by thermal otolith marks from 53% of the chum, 18% of the sockeye, 9% of the coho, and 50% of the Chinook salmon. Onboard stomach analysis of 63 potential predators, representing eight species, revealed one predation instance on juvenile salmon by a spiny dogfish (Squalus acanthias). Forecasting models using catch-per-unit effort (CPUE) of juvenile pink salmon in strait habitat of the northern region in 2003 and 2004 produced accurate predictions of southeastern Alaska pink salmon harvests in 2004 and 2005. However, the models using 2005 CPUE as a predictor overestimated harvest of pink salmon in 2006, indicating that CPUE alone is not sufficient to consistently predict year class strength. These results suggest that in southeastern Alaska, juvenile salmon exhibit seasonal patterns of habitat use and abundance, 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 better understand ecological interactions that affect interannual variation in salmon abundance and the role that salmon play in North Pacific marine ecosystems.