Dont plug the holes, but you need a new water pump. They are like 30 bucks at a parts store. The little holes let you know when the bearing seals are shot and water is seaping through them. Get a new water pump, plus it would be a waste to take off a water pump and not put a new one on, they are pretty much disposable on our cars. Kinda like spark plugs, if you take em out, mine as well put new ones in. But really get a new water pump and dont plug the small holes.