"Run Through" like a spear through the gizzard? or a child through a sand castle?
If you are asking if the scorpion will drown in the pond... No it won't so as long as he can climb back out. IME my scorps love the water the deeper the better, the deepest 'pond' I ever put in was 1/5 of a 20g L 4" deep.
Moving water is an excellent way to keep higher humidity levels (hence why those reptile waterfalls work so wonderfully). The petstores around here use an air pump and a hose to sorta move the water.
And Thaedion's right. Your scorpion won't drown in the water, unless it can't get out for some reason. If you put one in, just watch it for the first little bit to see if it has any problems, but almost guarenteed, it'll be fine.
If you're really worried, just slant a rock at the far end of the 'pond', so that the scorpion can climb out.