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While it has long been known that Pacific salmon use estuarine habitat, it has proven much harder to establish that the loss of estuarine habitat results in reduced survival. We used coded-wire tagging of hatchery fish to estimate the survival from release until maturity and related this survival to several indicators of estuarine condition. We found a significant relationship between the survival of chinook salmon (Oncorhynchus tshawytscha) and the percentage of the estuary that is in pristine condition, but no significant relationship for coho salmon (Oncorhynchus kisutch). This supports field observations that chinook salmon use estuarine habitat much more than coho salmon and confirms that the loss of estuarine habitat results in lower survival of chinook salmon.