Are there any special rules to be aware of in order to do Tevilath Keilim in a creek or other natural body of water, as compared to a Mikvah?
There are 2 types of Mikvahs:
Mayim Chayim: which is a flowing spring. If the river's or creek's sources are mainly spring fed (and not rain water, or melted snow from mountains), then that would be a kosher mikvah.
Boros created by people filled with rainwater (not drawn). (Sorry I don't know the exact technical term- it may bor hashaka and bor zeriya). This type of mikvah cannot have any water leaking in or out of it from the ground (although water can flow in from the sky). I don't think anything like this could occur in nature (but I'm not sure).
As far as special rules for natural bodies of water (mayim chaim), our Rav mentioned that certain of the poskim he consults with have a concern about doing tevila in a natural body after a heavy rain. If your dunking in water which is majority of rain water, then your tevila will be posul.