Juvenile Pacific salmon (Oncorhynchus spp.), ecologically-related species, and associated biophysical data were collected from the marine waters of the northern and southern regions of southeastern Alaska in 2009. This annual survey marks 13 consecutive years of systematically monitoring how juvenile salmon interact in marine ecosystems, and was implemented to identify the relationships among biophysical parameters that influence habitat use, marine growth, predation, stock interactions, and year-class strength of juvenile salmon. This report also contrasts the 2009 findings with selected biophysical parameters from the prior 12 sampling years. Up to 17 stations were sampled in epipelagic waters over four time periods (20 sampling days) from May to August. Typically, 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, a water sampler, and a conductivity-temperature-depth profiler. Surface (3-m) temperatures and salinities ranged from approximately 8 to 15 ºC and 19 to 31 PSU from May to August. Nearly 11,000 fish, representing 12 taxa, were captured in 60 rope trawl hauls in July and August in the two regions. No trawling was conducted in June, in contrast to all other years. Juvenile salmon comprised about 97% of the total fish catch. Juvenile pink (O. gorbuscha), chum (O. keta), sockeye (O. nerka), and coho salmon (O. kisutch) occurred in 5698% of the trawls, while juvenile Chinook salmon (O. tshawytscha) occurred in < 13% of the hauls. All juvenile salmon species occurred more frequently in northern region trawls than in southern region trawls in July. In the northern region, catch rates of juvenile pink, chum, and coho salmon were higher in July than in August, whereas catches of sockeye salmon were higher in August. Coded-wire tags were recovered from 18 juvenile coho salmon from hatchery and wild stocks originating in southeastern Alaska. Alaska enhanced stocks were also identified by thermal otolith marks from 47% of the chum and 18% of the sockeye salmon examined. Onboard stomach analysis of 108 potential predators, representing seven species, did not provide evidence of predation on juvenile salmon. Biophysical measures from 2009 differed from prior years, in many respects. Integrated (20-m) temperature anomalies were all positive and salinity anomalies were negative; in particular, the May temperature anomaly was the 2nd highest on record. Anomalies of zooplankton total density were positive each month, a trend which has persisted for four years. In addition, size anomalies for juvenile salmon were positive, a shift from the previous two years. Condition residual anomalies were unusually high for juvenile salmon species in August. These data, in conjunction with basin-scale biophysical parameters, are currently being used to forecast pink salmon harvest in southeastern Alaska. Long-term monitoring of key stocks of juvenile salmon, on seasonal and interannual time scales, will enable researchers to understand how growth, abundance, and ecological interactions affect year-class strength of salmon and to better understand their roles in North Pacific marine ecosystems.