More peer reviewed fisheries science conclusions on the decline of Puget Sound steelhead.
Note they don't mention anything about over harvest as a contributing factor for the decline.

http://www.fws.gov/wafwo/fisheries/Publications/FP149.pdf


Habitat Conditions
Habitat utilization by steelhead has been most dramatically affected by a number of large
dams in basins feeding Puget Sound. In addition to eliminating accessibility to habitat, dams
affect habitat quality through changes in river hydrology, temperature profile, downstream gravel
recruitment, and the movement of large woody debris.
Many of the lower reaches of rivers and their tributaries in Puget Sound have been
dramatically altered by urban development. Urbanization and suburbanization have resulted in
the loss of historical land cover in exchange for large areas of imperious surface (buildings,
roads, parking lots, etc.). The loss of wetland and riparian habitat has dramatically changed the
hydrology of many urban streams, with increases in flood frequency and peak flow during storm
events and decreases in groundwater driven summer flows (Moscrip and Montgomery 1997,
Booth et al. 2002, May et al. 2003). Flood events result in gravel scour, bank erosion, and
sediment deposition. Land development for agricultural purposes has also altered the historical
land cover; however, because much of this development took place in river floodplains, there has
been a direct impact on river morphology. River braiding and sinuosity have been reduced by
dikes, hardening of banks with riprap, and channelizing the main stem. Constriction of the river,
especially during high flow events, increases likelihood of gravel scour and the dislocation of
rearing juveniles. Side channels are spawning habitat for steelhead and other salmonids.
Additionally, side channel areas provide juvenile rearing habitat, especially overwintering habitat
(Beechie et al. 2001, Collins and Montgomery 2002, Pess et al. 2002).
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There are two major dams in the Nooksack Basin, the Nooksack Falls power plant
diversion dam (completed 1906) above the impassable Nooksack Falls at river kilometer (RKM)
104.6 and the water diversion dam (1960) on the Middle Fork Nooksack River (RKM 11.6). The
Nooksack Falls project is upstream of an inaccessible falls and has been out of operation since a
fire in 1997; however, there is concern that renewed operation may alter natural flows. The
water diversion dam on the Middle Fork Nooksack River currently prevents upstream access to
historical steelhead habitat; furthermore, the dam diverts a considerable proportion of the
summer flow to Lake Whatcom for eventual use by the City of Bellingham (Smith 2002).
Comanagers currently are evaluating the passage of salmon and steelhead over the Middle Fork
Diversion Dam.
The Skagit River Basin contains two dam complexes, the Lower and Upper Baker dams
on the Baker River, and the Ross, Diablo, and Gorge dams on the Skagit River. Lower Baker
Dam was completed in 1927 at RKM 1.8 of the Baker River. Passage above the dams is
accomplished through a trap and haul program and downstream passage is accomplished via a
smolt collection facility at Upper Baker Dam (known as the “gulper”). Passage efficiency is
higher for larger (yearling) smolts that migrate near the surface, for example, coho salmon,
sockeye salmon (O. nerka), and steelhead, than for subyearling smolts of Chinook salmon, chum
salmon (O. keta), and pink salmon (O. gorbuscha). The other dam complex, incorporating the
Ross, Diablo, and Gorge dams, limits access at RKM 155.3 on the Upper Skagit River.
Surveys undertaken during the 1920s, prior to the construction of the first of the dams,
report steelhead were not present at or above the proposed location of the dams (Smith and Royal
1924). Similarly, the Seattle City Light diversion dam on the South Fork Tolt River in the
Snohomish River basin is located above the limit of steelhead migration (an impassable waterfall
is located at RKM 12.9). While these dams do not limit the habitat accessibility, they can affect
downstream steelhead population through changes in flow, or by blocking downstream
recruitment of gravel and large woody debris.
Landsburg Dam (RKM 35.1) on the Cedar River has blocked steelhead access to
approximately 27.4 km of mainstem habitat since 1900. Preliminary studies are currently
underway to provide passage for steelhead and other salmonids above the dam. Plans are also
being studied for restoring passage to the upper Green River. In 1913 the Tacoma Water
Headworks Diversion Dam eliminated access to 47.9 km of mainstem habitat. The construction
of Howard Hanson Dam (RKM 98.1) above the diversion dam in 1962 blocked access to several
kilometers of mainstem and tributary habitat (Kerwin and Nelson 2000). It is thought a summer
run of steelhead historically existed in the Green River, but that the run was extirpated following
loss of access to headwater spawning areas following the construction of the diversion dam.
The Buckley Diversion Dam (RKM 39.1, completed 1911) and the Mud Mountain Dam
(RKM 47.6, completed 1942) impede upstream passage on the White River. Returning adults
are collected at a trap associated with the Buckley Diversion Dam and trucked around both dams.
Downstream smolt passage occurs through the dams rather than through a trap and haul system.
In addition to upstream and downstream migration effects on salmonids, flow diversion and
ramping rates can result in dewatered redds, fish strandings, delayed migration, and degraded
water conditions. In the Puyallup River Basin, the Electron Dam (RKM 67.3) has blocked
upstream passage for more than 90 years. Construction of a fish ladder in 2000 has provided
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access over 16 km of mainstem habitat. Adult and juvenile fish passage studies are currently
underway.
In the Nisqually River Basin, the LaGrande Dam (RKM 63.5, completed 1945) and Alder
Dam (RKM 66, completed 1944) block upstream migration. At present there are no plans to
provide passage around these dams.
The two Cushman dams, Dam No. 1 (RKM 31.5, completed 1926) and Dam No. 2 (RKM
27.8, completed 1930) eliminated steelhead access to much of the North Fork Skokomish River.
Anecdotal evidence suggests steelhead utilized much of the North Fork, although it is not clear
whether these were winter or summer run fish. Additionally, the diversion of flow from the
North Fork to the powerhouse has reduced the overall flow of the Skokomish River by 40%
(USFS 1995).
In the Elwha River Basin, two dams, the Elwha (RKM 7.9, completed 1911) and the
Glines Canyon (RKM 21.6, completed 1927) block access to more than 100 km of historical
mainstem and tributary habitat. Both dams are scheduled for removal beginning in 2012.