If you are in a cove.....or even on a straight beach with a dock. Just start your boat, put it in gear while still tied to the dock and run it a little over idle speed with the wash going from deeper water towards the shore. This will start a current that will replace all the water in shallow areas with clean water. If you have an outboard, you can run it for quite a while, but inboards don't have as effective of a cooling system so you don't want to run it for more than 10 or 15 minutes or at least watch your temp gauge.
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