If it is just a tarp then it should be OK. I use a tarp on mine and hold the edges down with the water filled bags and sand bags. The tarp rests on top of the water so water on the top of the tarp won't make a difference. Actually helps hold it down in the wind.

If you have a safty cover that is taunt and is not supposed to rest on top of the water, then you should drain it off or you will end up possibly damaging the springs that hold it on.

Bruce