Primary production due to phytoplankton can be very high in these shallow 
embayments over the entire water column during spring and summer. This 
process can utilize nutrients faster than they can be supplied by a net 
water exchange with the main parts of the Sound. During the periods of 
high primary production the surface waters become supersaturated with dis¬ 
solved oxygen. As this production wanes due to die off and grazing, 
dissolved oxygen can decrease at depth while nutrients increase. 
The sediments in the heads of these quiet protected bays are generally 
fine and high in organic content. Other regions of these bays have mixed 
coarse to fine sediments that are representative of the adjacent land 
materials and little wave or current energy is present to erode and sort 
beach material. It is in these bays that the native shellfish are found 
and shellfish aquaculture occurs. 
Because primary production appreciably depletes soluble nutrients in these 
shallow appended embayments and natural water exchange rates are reduced, 
anthropogenic sources of nutrients can play a significant role in in¬ 
creasing primary production above normal levels to cause eutrophication. 
These inlets are poor sites for sewage treatment plant outfalls or 
drainage systems that conduct water laced with nutrients from land areas 
of intensive human use. Fortunately for Puget Sound most of these shallow 
embayments are surrounded by rural rather than urban and industrialized 
land usage. However drainage from the land, even under rural conditions, 
can supply coliform bacteria having its source in failing septic tank 
systems or hobby farms. Coliform bacteria derived from fecal matter of 
warm-blooded animals is not normally detrimental to the valuable shell¬ 
fish resources, but its presence above certain concentration levels can 
cause health risk concerns and result in the closure of shellfish beds 
to commercial and recreational harvest. 
The reduced net exchange of water between these shallow inlets and the 
main channels of the Sound not only restricts the natural supply of 
nutrients for in situ primary production, it also restricts the exporting 
of phytoplankton from the embaj^ents. This is why the shellfish have such 
a good food supply and why sediments in these bays are high in organic 
content. The sediments, being high in organic content, are often anoxic 
a few inches below their surface. Over the fall and winter period, when 
light levels and productivity are reduced and stream flow and wave 
activity increases, these inlets gradually regain reasonable levels of 
dissolved oxygen and nutrients in readiness for a new spring bloom. 
The main channels of Puget Sound function quite differently than the small 
appended embayments. In the main basin of Puget Sound the direct measure¬ 
ment of currents and their integration over tidal months as well as water 
and salt budget analysis (Cannon, 1983, Collias, 1977, Friebertshauser and 
Duxbury, 1972, and Barnes and Ebbesmeyer, 1978) indicate that a net two-layer 
estuarine circulation exists. There is a net seaward flux in the upper 
150 ft. of the water column and a landward flux between 150 ft. depth and 
the channel bottom at 600 to 800 ft. depth. It must be appreciated that 
depths of 600 ft. or greater are equivalent to the depth of the outer 
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