I actually used to have this problem as a child, and I believe it was largely due to the fact that I had terrible ear infections. I hated getting water in my ears. I also hated getting it in my nose, but I think I was more terrified of getting it in my ears (because many times, I'd end up with an ear infection later).
Try some ear plugs that really fit well—maybe some wax ones that can conform to his ear shape and keep the water out. Does he get ear infections? That could be the reason. Some kids are just scared of water, though, and the only way to fix that is to get them used to it, I'd imagine. They just have to be around water more. I developed a slight fear of water because of my ear issue (and, of course, scary movies that involved scary things in water didn't help, either). Once I was around water a lot more, I became less and less scared. It takes time, but he can grow out of it. Poor kid.