I can save you a lot of trouble. Don't bother pumping the water, just bathe in the creek. Use a biodegradable soap. It is "camping" right? Why not rough it? You can get a good shower when you get home.
As a kid I swam in the Ohio River, Wheeling Creek, Fish Creek and numerous local lakes and strip ponds. I can rattle off names of a hand-full of buddies who were right there beside me and are still alive today. I don't remember any of us ever getting sick?
As an adult, I still wade in streams while fishing, water ski lakes and paddle many creeks and rivers. During warm weather, most of these trips include a dunk or two, whether intentional or not. Thousands of rafters hit our white water annually.
For goodness sake, use the water. It wouldn't hurt to take a few precautions because it's going into your camper's water system.
I would pump to a primary tank. Maybe get a plastic barrel and cut it in half. Disinfect this water with bleach, iodine or some other water treatment chemical. Then pump that to your fresh tank. When done, the hose and pump go right into the barrel for storage. Disinfect barrel prior to each use.
My MH has the tank and pump just inside a storage bay. I have a "T" there that is used for winterizing. I place a 5-gallon water jug on the ground and use my system to pump that to my fresh water tank. It is the same as pumping antifreeze except I turn the lever to "tank fill" and wallah, the water goes into my tank.
If you have a similar set up, use a pump as already noted here from the creek and pump to the barrel. Use your onboard pump or a second one to pump to your system.
They make pumps that are run by a drill. You could use that to pump up to your fresh water fill tube. Generator could be used for a 110V drill or to recharge one.
When I tie a lure on my fishing line, I sometimes use my teeth! I know, GASP!
Years ago in Guatemala, about 20 Soldiers (me included) got deathly ill with an intestinal disease. Turns out, they pumped the porta-jons out onto a soccer field to make the grass grow real green. Yuck. You want to talk about sick. Many of us needed medical treatment. I knew I was in for it when I noticed our tennis shoes were turning bright blue.
That hasn't changed the way I enjoy our wonderful waterways here. You all are missing out if you're afraid to get in the water.