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Most rivers take several days to drop back to normal color after big rain events, give the sound a few extra days to settle out on top of that, so maybe a week after a big rain event. The Snoqualmie hit flood stage over the weekend, so it will take a bit longer for all of that crap to flush out.
 

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It can take as little as one good incoming tide.
SF
Exactly! I am on the west side of Camano and can see the mud coming around the corner from the north end, a big and very distinct line between mud and blue water. Most times, it only comes so far south and the the tide changes and it is gone. Of course the north sound flushes pretty well, even in Saratoga passage. the dirty water here generally comes from beach erosion fron big breezes. Havimg said that, on the east side of the island, the Stilly has it's way, it can stay brown and nasty for weeks.
Obviously, it just depends on where you are.
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I believe the east side Whidbey beaches will clear pretty quickly after the rain, again, that is Saratoga passage and it flushes pretty well. Not so certain about Holmes harbor, less current and a fair amount of runoff make that a little more difficult. While on the East side of Whidbey, enjoy the "Sound of Freedom", lots of fighter activity lately :).
 

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Most of the mud in Puget Sound is actually in a thin layer of freshwater that floats on saltier, denser water in the sound. One good tidal exchange or some wind aided mixing can clear that muddy layer away by mixing it into the clear marine layers.

This is not always true for shallow bays, muddy shorelines, etc.. those can stay muddy for different reasons.
 
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