Until recently, research on mortality of anadromous fishes in the marine environment was largely limited to estimates of total mortality and association with group characteristics or the environment. Advances in sonic transmitter technology now allow estimates of survival in discrete marine habitats, yielding important information on species of conservation concern. Previous telemetry studies of steelhead Oncorhynchus mykiss smolts in Puget Sound, Washington, USA indicated that approx. 80% of fish entering marine waters did not survive to the Pacific Ocean. The present study re-examined data from previous research and incorporated data from additional Puget Sound populations (n = 7 wild and 6 hatchery populations) tagged during the same period (2006−2009) for a comprehensive analysis of steelhead early marine survival. We used mark-recapture models to examine the effects of several factors on smolt survival and to identify areas of Puget Sound where mortality rates were highest. Wild smolts had higher survival probabilities in general than hatchery smolts, with exceptions, and wild smolts released in early April and late May had a higher probability of survival than those released in early and mid-May. Steelhead smolts suffered greater instantaneous mortality rates in the central region of Puget Sound and from the north end of Hood Canal through Admiralty Inlet than in other monitored migration segments. Early marine survival rates were low (16.0 and 11.4% for wild and hatchery populations, respectively) and consistent among wild populations, indicating a common rather than watershed-specific mortality source. With segment-specific survival information we can begin to identify locations associated with high rates of mortality, and identify the mechanisms responsible.