Biophysical data were collected along a primary marine migration corridor of juvenile Pacific salmon (Oncorhynchus spp.) in the northern region of southeastern Alaska at 20 stations in five, six-day sampling intervals from May to September 2000. This survey marks the fourth consecutive year of systematic monitoring, and was implemented to identify the relationships among biophysical parameters that influence the habitat use, marine growth, predation, stock interactions, year-class strength, and ocean carrying capacity of salmon. Habitats were classified as inshore (Taku Inlet and Auke Bay), strait (Chatham Strait and Icy Strait), and coastal (Cross Sound and Icy Point), and were sampled from the National Oceanic and Atmospheric Administration ship John N. Cobb. At each station, fish, zooplankton, surface water samples, and physical profile data were collected during daylight using a surface rope trawl, conical and bongo nets, and a conductivity-temperature-depth profiler. Surface (2-m) temperatures and salinities during the survey ranged from 6.6 to 14.1°C and 11.5 to 32.0 PSU. A total of 7,920 fish and squid, representing 30 taxa, were captured in 89 rope trawl hauls from June to September. Juvenile Pacific salmon comprised 86% of the total catch and were the most frequently occurring species: pink (O. gorbuscha; 60%), chum (O. keta; 55%), coho (O. kisutch; 49%), sockeye (O. nerka; 47%), and chinook salmon. Of the 6,846 salmonids caught, > 99% were juveniles. Non-salmonid species making up > 2% of total catch included walleye pollock (Theragra chalcogramma), Pacific herring (Clupea pallasi), and soft sculpin (Psychrolutes sigalutes). Temporal and spatial differences were observed in the catch rates, size, condition, stock of origin, and predation rates of juvenile salmon species. Catches of juvenile chum, pink, and coho salmon were highest in July, whereas catches of juvenile sockeye and chinook salmon were highest in June and September, respectively. By habitat type, juvenile salmon except chinook were most abundant in straits; juvenile chinook salmon were most abundant in inshore habitat. In the coastal habitat, catches along the Icy Point transect were highest within 40 km of shore. Size of juvenile salmon increased steadily throughout the season; mean fork lengths (mm) in June and September were: pink (95 and 198), chum (106 and 218), sockeye (114 and 196), coho (166 and 285), and chinook salmon (157 and 264). Coded-wire tags (CWTs) were recovered from seven juvenile and one immature chinook; only one was of non-Alaska origin, a juvenile chinook from the Columbia River Basin recovered in September. CWTs were recovered from seven juvenile and two adult coho; all were of Alaska origin. In addition, otoliths of 1,260 juvenile chum and 401 juvenile sockeye salmon revealed that 59% and 27% of these fish were Alaska hatchery stocks represented by thermal marks. Onboard stomach analysis of 214 potential predators, representing eleven species, indicated that 11% of adult coho salmon, 4.5% of spiny dogfish (Squalus acanthias), and 1% of adult walleye pollock preyed on juvenile salmon. Our results suggest that, in southeastern Alaska, juvenile salmon exhibit seasonal patterns of habitat use synchronous with environmental change, and display species- and stock-dependent migration patterns. Long term monitoring of key stocks of juvenile salmon, both on intra- and interannual bases, will enable researchers to understand how growth, abundance, and ecological interactions affect year-class strength and ocean carrying capacity for salmon.