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The geologic origin
of the Bolinas Lagoon has its roots in one of Earth's most fundamental
and unique processes - continental drift. A theory for hundreds of years,
the mobility of continents was proved only 30 years ago. It is now known
that the whole of the Earth's crust, both under the ocean as well as land,
is broken up into ten large and many smaller 'plates', which float on
a layer of melted rock- magma- the consistency of toothpaste.
Each plate glides across the planet in its own direction and at its own pace. The different trajectories of the plates may take them on a collision course, in which mountains form along the edges of the crumpled continents. Alternatively, two plates may drift apart, allowing underlying magma to seep through the crack and new crust to form in between. A third possibility is that plates may slide laterally past each other. This transform boundary is associated with earthquakes, which occur when overlying rock strata is stressed to the breaking point by the opposing forces beneath. Many small, frequent quakes may continually release the stress of the conflicting forces, or a large slippage may occur all at once, resulting in large, damaging quakes.
The unique geologic composition of the Bolinas Lagoon Watershed reflects
the transverse faulting of the San Andreas Valley. The western portion
of the Bolinas Lagoon Watershed is situated on the Pacific Coast Plate,
which is slowly creeping northwest. East of the lagoon, the watershed
is part of the North American Plate, which is heading in a southwesterly
direction. 
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Semi-enclosed coastal water, open to the sea, having a high freshwater
drainage and marked cyclical fluctuations in salinity - usually the mouth
of a river.
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The 'flyway' concept is a human construct, originally developed by waterfowl
biologists to describe the general migratory patterns of 
ducks.
Three major flyways have been described in North America:
From
birth, lagoons are swaddled in sediments. Sand from the ocean, and rock,
minerals and organic material from fresh water creeks swirl constantly
into the lagoon. Because sediments are heavier than water, they tend to
settle out of the water, a process called sedimentation. Where these sediments
finally settle effects the nature of the lagoon, its ecosystem, and its
future. When the sediment deposits build to a height that severs the sea's
influence, the lagoon dies.
Many factors affect sedimentation. For example, because
fresh water is lighter than seawater, creek sediments don't mix with the
denser, saltier water of the lagoon but 'float' towards its center. The
faster the creek flows, the further the sediments will be carried away
from the creek mouth. During times of heavy rains creek sediments may
even be carried directly out to the ocean, with no chance to settle within
lagoon boundaries. Slower creek flows encourage settlement within the
lagoon. When creek flow is low, sediments settle near creek mouths, often
at the far reaches of the lagoon. Increased sediments accelerate plant
growth, which perpetuates the problem by holding on to bottom materials
with their root systems.
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When the masses of continents interact, their shapes evolve. Mountains
and valleys are formed. During earthquakes, sections of the earth may
drop many feet. The San Andreas Fault Valley was and is still being shaped
by this process.
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The volume of water exchanged on tide cycles. In Bolinas Lagoon, currently,
of 3 million cubic yards, on average, down from an estimated 7.4 million
cubic yards originally, and being reduced at a rate of 52,000 cubic yards
per year.
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