EPA's Vessel General Permit and Small Vessel General

occurs in residence time in fresh water and estuarine environments. For example, Hayman et al.,
(1996) described three juvenile Chinook salmon life histories with varying residency times in the
Skagit River system in northern Puget Sound. Chinook salmon utilize nearshore Puget Sound
habitats year-round, although they can be far from their natal river systems (Brennan et al. 2004).
Status and Trends
NMFS listed Puget Sound Chinook salmon as threatened in 1999 (64 FR 14308); that status was
reaffirmed on June 28, 2005 (70 FR 37160). This ESU has lost 15 spawning aggregations (nine
from the early-run type) that were either independent historical populations or major components
of the remaining 22 existing independent historical populations identified (Good et al. 2005).
The disproportionate loss of early-run life history diversity represents a significant loss of the
evolutionary legacy of the historical ESU.
Data reported by Good et al., (2005) indicate that long term trends in abundance for this ESU are
split with about half of the populations declining, and the other half increasing. In contrast, the
short-term trend for four populations is declining. The overall long-term trend in abundance
indicates that, on average, populations are just replacing themselves. Estimates of the short-term
median population growth rate (λ) (data years 1990-2002) indicate an even split between
populations that are growing and those that are declining, although estimates would be lower for
several populations if the fraction of naturally spawning hatchery fish were available for all
populations within the ESU. For available data, when λ is calculated assuming that hatchery fish
have the equivalent success of natural spawners then the largest estimated decline occurs in the
Green River. Populations with the largest positive short and long-term trends include the White
River and the North Fork Nooksack River (Good et al. 2005). Lambda for the Skagit River,
which produces the most Chinook salmon in this ESU, has increased slightly. Overall, the recent
analysis by Good et al., (2005) illustrated that there has not be much change in this ESU since
NMFS’ first status review (Busby et al. 1996). Individual populations have improved, while
others have declined. However, the lack of information on the fraction of naturally spawning,
hatchery-origin fish for 10 of the 22 populations within this ESU limits our understanding of the
trends in naturally spawning fish for a large portion of the ESU.
The estimated total run size of Chinook salmon in Puget Sound in the early 1990s was 240,000
fish, representing a loss of nearly 450,000 fish from historic numbers. During a recent 5-year
period, the geometric mean of natural spawners in populations of Puget Sound Chinook salmon
ranged from 222 to just over 9,489 fish. Most populations had natural spawners numbering in
the hundreds (median recent natural escapement is 766), and of the six populations with greater
than 1,000 natural spawners, only two have a low fraction of hatchery fish. The populations with
the greatest estimated component of hatchery fish tend to be in mid- to southern Puget Sound,
Hood Canal, and the Strait of Juan de Fuca regions. Estimates of the historical equilibrium
abundance, based on pre-European settlement habitat conditions, range from 1,700 to 51,000
potential Puget Sound Chinook salmon spawners per population. The historical estimates of
spawner capacity are several orders of magnitude higher than spawner abundances currently
observed throughout the ESU (Good et al. 2005).
78