426 
Seasonal and interannual variation 
in juvenile salmonids and associated fish assemblage 
in open waters of the lower Columbia River estuary 
Email address for contact author: laurie.weitkamp@noaa.gov 
1 Conservation Biology Division 
Northwest Fisheries Science Center 
National Marine Fisheries Service 
Newport Research Station 
2032 SE Marine Sciences Drive 
Newport, Oregon 97365 
2 Fish Ecology Division 
Northwest Fisheries Science Center 
National Marine Fisheries Service 
Point Adams Research Station 
520 Heceta Place 
Hammond, Oregon 97121-0155 
3 Cooperative Institute for Marine Resources Studies 
Hatfield Marine Science Center 
Oregon State University 
2030 SE Marine Sciences Drive 
Newport, Oregon 97365 
Abstract — The transition between 
freshwater and marine environments 
is associated with high mortality 
for juvenile anadromous salmonids, 
yet little is known about this criti- 
cal period in many large rivers. To 
address this deficiency, we investi- 
gated the estuarine ecology of juvenile 
salmonids and their associated fish 
assemblage in open-water habitats 
of the lower Columbia River estuary 
during spring of 2007-10. For coho 
(Oncorhynchus kisutch), sockeye (O. 
nerka), chum (O. keta ), and yearling 
(age 1.0) Chinook ( O . tshawytscha) 
salmon, and steelhead (O. mykiss ), we 
observed a consistent seasonal pat- 
tern characterized by extremely low 
abundances in mid-April, maximum 
abundances in May, and near absence 
by late June. Subyearling (age 0.0) 
Chinook salmon were most abundant 
in late June. Although we observed 
interannual variation in the presence, 
abundance, and size of juvenile salmo- 
nids, no single year was exceptional 
across all species-and-age classes. We 
estimated that >90% of juvenile Chi- 
nook and coho salmon and steelhead 
were of hatchery origin, a rate higher 
than previously reported. In contrast 
to juvenile salmonids, the abundance 
and composition of the greater estua- 
rine fish assemblage, of which juve- 
nile salmon were minor members, 
were extremely variable and likely 
responding to dynamic physical con- 
ditions in the estuary. Comparisons 
with studies conducted 3 decades ear- 
lier suggest striking changes in the 
estuarine fish assemblage — changes 
that have unknown but potentially 
important consequences for juvenile 
salmon in the Columbia River estuary. 
Manuscript submitted 17 January 2012. 
Manuscript accepted 22 August 2012. 
Fish. Bull. 110:426-450 (2012). 
The views and opinions expressed 
or implied in this article are those of the 
author (or authors) and do not necessarily 
reflect the position of the National Marine 
Fisheries Service, NOAA. 
Laurie A. Weitkamp (contact author ) 1 
Paul J. Bentley 2 
Marisa N. C. Litz 3 
The Columbia River was historically 
home to one of the largest Pacific 
salmon ( Oncorhynchus spp.) runs in 
the world, with 10-16 million adult 
salmon and steelhead (hereafter 
collectively referred to as salmon) 
returning to the basin annually before 
European settlement (NRC, 2004). As 
human population and activities have 
increased over the last century (Sher- 
wood et ah, 1990; NRC, 1996), Colum- 
bia River salmon runs have declined 
to the point that adult returns are 
typically less than 10% of historical 
levels (PFMC, 2011). Furthermore, 
more than half of the salmon popula- 
tions in the river basin are thought 
to have become extinct (Gustafson et 
ah, 2007), and most extant wild popu- 
lations receive protection under the 
U.S. Endangered Species Act (ESA) 
as threatened or endangered species 
(Ford, 2011). This protected species 
list includes 5 subgroups of steelhead 
([O. mykiss]', lower, middle, and upper 
Columbia River and Snake and Wil- 
lamette rivers) and 1 subgroup each 
of coho ([O. kisutch]', lower Colum- 
bia River), chum ( [ O. keta]; Colum- 
bia River), and sockeye ( [O. nerka]; 
Snake River) salmon (Ford, 2011). 
Also listed are 5 subgroups of Chi- 
nook salmon (O. tshawytscha ): lower 
Columbia River, Snake River spring 
and summer, Snake River fall, upper 
Columbia River spring, and upper 
Willamette River (Ford, 2011). These 
Chinook salmon subgroups display 
diverse life-history variation, includ- 
ing the timing of adults returning 
to freshwater (indicated by season 
[i.e., spring, summer, or fall] in sub- 
group names (e.g., Snake River fall) 
and age of ocean entry for juveniles 
(fall runs have subyearling [age 0.0] 
smolts, spring runs have yearling [age 
1.0] smolts, and smolt age of summer 
runs vary by group) (Myers et al., 
1998). There is no recognized pink 
salmon (O. gorbuscha ) population in 
the Columbia River basin, although 
individuals often are observed (Hard 
et al., 1996; Gustafson et al., 2007). 
Because of these listings, considerable 
time and resources have been devoted 
to defining and implementing actions 
that will help restore salmon popula- 
tions in the Columbia River. 
