We monitored fish assemblages monthly at estuarine and tidal freshwater sites in the lower Columbia River and estuary from January 2002 through September 2007 in order to identify specific salmon stocks and migration stages that may benefit from habitat restoration initiatives. We report landscape‐scale and seasonal variation in abundance, size, hatchery production (based on adipose fin clips), and genetic stock of origin of juvenile Chinook salmon Oncorhynchus tshawytscha. From fish implanted with coded wire tags (CWTs), we also determined the sites of release and inferred migration patterns. Chinook salmon were found in diverse life history stages and forms, including fry migrants, fingerlings, and (fewer) yearlings. Abundance increased in February and decreased in August, but salmon were present in all months each year. Spatial gradients in abundance and size were strong, with fewer but larger fish in brackish than in tidal freshwater zones. Overall, 30% of the Chinook salmon measured were fry (≤60 mm) that were likely naturally produced fish. These occurred at higher mean monthly proportions in tidal freshwater than in estuarine zones. In contrast, most larger fish were probably raised in hatcheries. Genetic stock assessment revealed that the majority of the Chinook salmon analyzed were from fall‐run stock groups originating in the lower Columbia River, with 15% originating from other stock groups. Of these minority contributors, about 6% were identified as upper Columbia River summer–fall‐run Chinook salmon while seven other stock groups accounted for the remainder, including 3% from transplants originating in southern Oregon's Rogue River. Recaptures of tagged fish revealed maximum migration times of 143 d for subyearlings and 52 d for yearlings, and both CWT and genetic data indicated that fall Chinook salmon from coastal rivers occasionally entered the estuary. These data demonstrated a widespread temporal and spatial distribution of subyearling Chinook salmon in shallow‐water habitats of the lower Columbia River and estuary. Received June 28, 2011; accepted February 28, 2012

Extensive efforts are underway to restore and conserve nearshore shallow water habitats in the Columbia River estuary with the intent of increasing the estuary's capacity to provide food, refuge, and other crucial ecosystem functions for juvenile salmon. Juvenile Chinook Salmon Oncorhynchus tshawytscha, including those from the five Evolutionarily Significant Units listed as threatened or endangered under the U.S. Endangered Species Act, are particularly expected to benefit from the habitat improvements. However, information on the temporal and spatial estuarine distributions of juveniles from specific populations or stocks is lacking and impedes restoration planning for at‐risk salmon. We conducted a series of surveys to sample juvenile Chinook Salmon occupying shallow‐water habitats with sandy beaches in six hydrogeomorphic reaches across the tidal freshwater portion of the estuary and also at one long‐term reference site near the estuary mouth. Sites were sampled bimonthly over 26 months during 2010–2012 to capture seasonal patterns of stock‐specific habitat use. Genetic stock identification analyses were conducted on the samples using microsatellite DNA loci and genotypic data representing spawning populations from throughout the Columbia River basin. We identified three tidal freshwater areas that could be distinguished by genetic stock composition. Lower tidal freshwater reaches were dominated by fall‐run juveniles from West Cascade tributaries (>70%), upper reaches had a large proportion of fish from the upper Columbia River summer–fall stock (>60%), and middle reaches were characterized by greater stock diversity with no single stock contributing more than 30% in each reach. Stock‐specific juvenile habitat use differed by season, life history type, and between natural and hatchery‐produced fish. Data from this study provide improved descriptions of the near‐shore estuary habitat use of several Columbia River genetic stocks of Chinook Salmon that can assist managers in the design and selection of estuary restoration projects.Received November 11, 2013; accepted February 18, 2014

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