I spent half my life in the water of the Bay since it was my front yard. I hope I don't get sick.
Our girls don't have the same experience tho. When my Husband was young he got a terrible ear infection that they said came from the Bay, so we just never took the kids, but only for that reason. (instead of the Bay, they got infections from pools, lol)
As far as the ALS/MS issues, sounds like maybe more of an air thing then water thing to me. It is my understanding that Mobile Bay 'flushes' out much quicker then other similar Bays.