16 year old fell in pond and health concerns?

In medicine there is always the possibility of something happening; but the odds are not too great. Your peds is correct; people through the ages have done much worse & been fine. The body has remarkable defenses to combat many things. There is nothing you can to do "prevent" an unknown disease or parasite such as a shot. He should just watch for unusual symptoms for a week or so (with out micro yzing everything). The slight itching and nausea do not sound terribly significant (at this time). But if things get worse, that is something that should be looked at.