Biology Reference
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of local streams and tributaries beneath the surface of the bay. All of this
changed after the California Gold Rush, whose miners washed away entire
hillsides in search of the yellow ore. Bruce Jaffe's research shows that sedi-
ment pouring down from the gold mines over three decades (1856-1887)
filled up the Petaluma River channel, more than doubled the acreage of
surrounding mudflats, and smothered San Pablo Bay with 230 million
cubic yards of soil from the Coast Ranges and Sierra uplands (see Figure 3).
The USGS's Jaffe notes that all of this deposition on the floor of the bay
100 years ago stopped around 1950. Then erosion began. As farmers
around the bay and river banks built dikes to drain land for agriculture
and to control flooding, and others upstream diverted river flows for
human uses, these waters were cut off from sediment supplies upstream
and along shores. Ninety acres of San Pablo Bay mudflats—those flat buf-
fer lands between bay and shore—disappeared every year between 1951
and 1983, says Jaffe.
Today's bay shallows remain at the mercy of the wind. When it's shal-
low, it's easier for the antics of the wind on the surface to roil the bottom.
In shallow parts of the bay, winds create waves that loop water up, down,
around, and back again—from surface to bay floor. And since these wind-
waves reach all the way down to the bottom, they also pick up and move
things on the bottom, like mud.
Sediment
For many people, brown water is a red flag. Water quality managers re-
ceive frequent reports of brown water from concerned locals who assume
it's a sewage leak or pollutant spill. San Francisco Bay is certainly more
brown and turbid (cloudy) than most estuaries. Even if the water is very
brown, it's generally not dirty or polluted, but filled with sediment. In-
deed, whatever the color—brown, green, grey, blue—most hues come
from suspended sediments and how they absorb and reflect light. Even a
small amount of sediment can reflect a lot of light. On the muddiest days
(usually in spring, when runoff volume is greatest), the amount of sedi-
ment in the water is well below 1 percent. USGS scientist David Schoell-
hamer, who has studied sediment transport in the bay, says if you flooded
an island with 10 feet of chocolate-hued water from the bay and let it settle
out, you'd wind up with less than a tenth of an inch of deposition on the
bottom.
Sediment is an important part of the bay's physical condition. The larg-
est concentrations appear on the surface with freshwater runoff in spring
and summer. By fall and winter, most of it has sunk down to the bottom or
 
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