I run my boat in silty water, so I flush it after nearly every outing just to keep anything from settling in the cooling system. I do so as soon as I get home from the lake, and make sure it gets warm enough to open the T-stat.
Do the same thing in salt water, as well as rinsing down the outdrive, etc. Tap water should work fairly well in killing micro-organisms from the sea water. When I was in the Navy, we would lay up idle sea water systems with tap water, and occasionally use concentrated juice drinks (High Citric Acid content) to keep the system from getting fouled.
I dicourage using a motor in sea water unless you have a heat exchanger due to the potential for fouling of difficult to flush areas inside the engine, etc.
Hope that helps.
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Walt B
"Debt-Charged"Black '07 H210SS6.2L Bravo One turning a 21P HIFive
Wakeboard Tower with Perfect Pass Stargazer version
Missouri River; Kansas City, Mo.