Intermittent fasting will not hurt your metabolism in any way, nor will it mess with your system. But as Stephanie said, it shouldn't be used as a quick fix.
A good way to test to see if you are indeed hanging on to water is to drop your carbohydrate level for a few days. This will have a diuretic effect, but your mileage may vary.
I'm in the middle of a stall myself. I really do believe that our bodies just need "breaks" occasionally, even if the science doesn't support me
Don't stress over it, because stress is going to make it that much harder to lose.