Weitkamp et ai.: Seasonal and interannual variation in juvenile salmonids in the lower Columbia River 
427 
Hatchery production of anadromous Pacific salmon in 
the Columbia River basin is extensive; the Fish Passage 
Center’s (FPC) database indicates that -140 million 
salmon smolts were released annually during 2007-10 
(FPC data available at http://fpc.org/, accessed July 
2011). These hatchery fish support commercial, tribal, 
and recreational fisheries in marine waters from Alaska 
to California, in addition to fisheries in the Columbia 
River (PFMC, 2011). Hatchery fish also dominate adult 
returns and contribute 34-50% of fall Chinook salmon 
to more than 80% of spring and summer Chinook and 
coho salmon returns to the Columbia River (NRC, 1996; 
ISAB 1 ). With the emphasis on restoring wild popula- 
tions, there is increasing concern about potentially neg- 
ative effects of hatchery fish on wild populations (NRC, 
1996; Rand et al., 2012). However, little is known about 
these interactions in migratory corridors or estuaries, 
where hatchery and wild populations that are spatially 
segregated in stream environments have opportunities 
to interact (Naish et al., 2008; Rand et al., 2012). This 
gap in knowledge is particularly notable in open-water 
habitats of the Columbia River estuary, where such 
basic information, such as the seasonal presence, rela- 
tive abundance, or potential size differences between 
hatchery and wild juvenile salmon, is lacking. 
As part of the effort to restore Columbia River salm- 
on, attention is increasingly focused on salmon when 
they are present in the estuary (Fresh et al., 2005; 
Bottom et al., 2005, 2006). The estuary phase and the 
initial ocean stage are viewed as “critical periods” of the 
salmon life cycle because they are periods of high mor- 
tality as salmon transition from freshwater to marine 
habitats (Pearcy, 1992; Schreck et al., 2006; Welch et 
al., 2008). For example, Kareiva et al. (2000) estimated 
that even minor (5%) improvements in estuarine and 
early ocean survival would reverse population declines 
in Columbia River spring and summer Chinook salmon. 
However, the causes for the mortality (e.g., predation, 
starvation, and disease) or the factors that increase 
or depress mortality in a given year are largely un- 
known. Furthermore, juvenile salmon are not the only 
fishes inhabiting estuaries, but rather they are minor 
members of a larger fish assemblage (Haertel and Os- 
terberg, 1967; McCabe et al., 1983; Bottom and Jones, 
1990). Therefore, understanding processes such as pre- 
dation on juvenile salmon requires understanding the 
dynamics of the larger fish community (Saunders et al., 
2006). A lack of such information has greatly frustrated 
managers who must identify actions that can be imple- 
mented to increase survival during this critical stage. 
Although mortality may be high in the estuarine 
environment, estuaries provide juvenile salmon with 
productive foraging opportunities, refuge from piscine 
predation (especially compared with marine waters), 
and offer intermediate environments during the physi- 
1 ISAB (Independent Scientific Advisory Board). 2011. Colum- 
bia River Basin food webs: developing a broader scientific 
foundation for fish and wildlife restoration. Doc. ISAB 2011-1. 
[Available at http://www.nwcouncil.org.] 
ological transition to salt water (Simenstad et al., 1982; 
Thorpe, 1994; Bottom et al., 2005). However, the degree 
of benefit likely varies by species and life history type, 
because some groups (e.g., subyearling Chinook salmon) 
make prolonged use of estuaries, whereas others (e.g., 
steelhead) largely pass through estuaries in a few days 
(Dawley et al. 2 ; Schreck et al., 2006; Campbell, 2010; 
Roegner et al., in press). Extensive research efforts in 
the Columbia River estuary from the late 1960s (John- 
sen and Sims, 1973) to the mid-1980s (McCabe et al., 
1983; Dawley et al. 2 ; Bottom and Jones, 1990) clearly 
established that most juvenile salmon migrating as 
yearlings (i.e., yearling Chinook and coho salmon and 
steelhead) passed rapidly through the estuary in the 
deep channels, bisecting an otherwise broad, flat estu- 
ary, where they were effectively caught with a purse 
seine. By contrast, most subyearling migrants (sub- 
yearling Chinook and chum salmon) occupied shallow 
waters close to shore. Most research efforts conducted 
since the 1980s have focused primarily on subyearling 
salmon in shallow-water habitats of the Columbia River 
estuary (e.g., Bottom et al., 2005; Craig, 2010; Roegner 
et al., 2010a, in press; Spilseth and Simenstad, 2010). 
In 2007, we re-initiated a study the estuarine fish 
assemblage in deep (-10 m) waters of the Columbia 
River estuary to address the deficiency of information in 
these habitats. Specifically, we wanted to characterize 
the presence and dynamics of juvenile salmon and the 
greater fish assemblage to which they belong during 
the spring salmon outmigration (mid-April through late 
June) and to explore if or how environmental variation 
may influence the patterns we observed. We were par- 
ticularly interested in the determination of the follow- 
ing aspects of salmon in the Columbia River estuary: 
1) species- or age-class-specific timing and abundance 
of juvenile salmon and their variation, 2) origins of 
juvenile salmon, with respect to both hatchery or wild 
origin, and geographic sources, 3) size distribution and 
condition of each species or age class of salmon and 
whether there were size differences between hatchery 
and wild fish, 4) composition and dynamics of other 
fishes sharing these open water habitats, and 5) the 
suitability of nonsalmonids as alternative prey for salm- 
on predators based on overlap in size. Given the mul- 
titude of changes that have occurred in the Columbia 
River basin and estuary over the last 30 years (e.g., 
Sherwood et al., 1990; NRC, 2004), we also wanted to 
compare our results with those from studies conducted 
3 decades earlier. This comparison allows us to identify 
how juvenile salmon and the larger estuarine fish com- 
munity may have changed and begins to provide insight 
regarding expected changes in the future. 
2 Dawley, E. M., R. Ledgerwood, T. H. Blahm, C. W. Sims, J. 
T. Durkin, R. A. Kirn, A. E. Rankis, G. E. Monan, and F. J. 
Ossiander. 1986. Migrational characteristics, biological 
observations, and relative survival of juvenile salmonids 
entering the Columbia River estuary, 1966-1983. Final 
report of research funded by Bonneville Power Administra- 
tion. [Available from Northwest Fisheries Science Center, 
2725 Montlake Blvd. E., Seattle, WA 98112], 
