Distribution, Size, and Origin of Juvenile Chinook Salmon in Shallow‐Water Habitats of the Lower Columbia River and Estuary, 2002–2007

Abstract

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

Shallow Tidal Freshwater Habitats of the Columbia River: Spatial and Temporal Variability of Fish Communities and Density, Size, and Genetic Stock Composition of Juvenile Chinook Salmon

“…Similarly, Quinones and Mulligan (2005) reported that juvenile Chinook Salmon densities were greater in the middle and upper reaches (including tidal freshwater) of the Smith River estuary (California) than in the lowest segments. Although our study areas (centered at rkm 125 and 195) were segregated by greater distances than those sampled by Roegner et al (2012) and Quinones and Mulligan (2005), the two areas did not differ in salmon density or in the proportional representation of sizeclasses among unmarked Chinook Salmon. Temporal trends in Chinook Salmon size in our study and that of Roegner et al (2012) were similar; fry were predominant during winter and spring, and fish size generally increased with time.…”

“…Although the environmental conditions (e.g., vegetation and hydrology) resulted in spatial segregation across the LCRE, we did not observe longitudinal "zonation" in the fish community. Across an approximately 60-km expanse of the LCRE, Roegner et al (2012) noted that Chinook Salmon from the tidal freshwater zone (near rkm 60) were more abundant and smaller than those sampled downriver at middle-and lower-estuary sites. Similarly, Quinones and Mulligan (2005) reported that juvenile Chinook Salmon densities were greater in the middle and upper reaches (including tidal freshwater) of the Smith River estuary (California) than in the lowest segments.…”

“…Research on juvenile salmon in the LCRE (e.g., Dawley et al 1986;Maier and Simenstad 2009;Spilseth and Simenstad 2011;Roegner et al 2012) has largely focused on the lowest 75 km of the Columbia River, where tidal forces dominate (Jay et al, in press). In contrast, the migratory characteristics of juvenile salmon and steelhead in shallow tidal freshwater habitats upstream of rkm 75, where riverine forces predominate (Jay et al, in press), are not well understood (ISAB 2000;ISRP 2004;Fresh et al 2005).…”

Comparative Use of Shallow and Deepwater Habitats by Juvenile Pacific Salmon in the Columbia River Estuary Prior to Ocean Entry

“…In light of these differences, future research efforts investigating the effects of hatchery programs on rebuilding threatened Columbia River salmon populations (e.g., Paquet et al 2011) should evaluate ecological interactions between hatchery-and naturally produced fish in estuarine and nearshore ocean habitats (Fresh 1997;Rand et al 2012). Furthermore, the extent to which fine-scale habitat use patterns observed in this part of the estuary apply to reaches further upstream is unclear (Roegner et al 2012;Teel et al 2014;Sather et al 2016); additional research is needed to elucidate patterns of habitat use elsewhere in the system. Finally, our data can also guide the design of restoration actions for multiple salmon stocks and runs in the Columbia River estuary and can inform the potential benefits of such efforts.…”

“…Catches were processed according to standard protocols (Roegner et al 2012;Weitkamp et al 2012). Juvenile salmon were anesthetized (tricaine methanesulfonate), identified to species, and measured to the nearest millimeter FL.…”