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I drained the fuel bowl and apart from some sediment, there isn't any separation of fluids. If there was water in it, wouldn't the diesel be floating on top of it?
After straining it to capture the sediment, can I just put it back into the tank?
Yes, the water would be at the bottom of the fluid and obvious. If you are concerned with disposing of the fluid, go ahead and pour it through a coffee filter. That will trap everything and you can pour it in the tank. I usually just dump mine into my spare diesel can that I use to start fires when burning brush.