Anything from a zip-lock type bag (double zips may be safer) to an Otter Box to a Pelican case.
This may be one of those times when you will not feel embarassed to be seen wearing a lanyard.
If you are thinking you will get more than a bit of light spray you might want to avoid leather, although if done properly you can soak them in saltwater and bring them back to life. My recommendation is kydex over nylon just because kydex does not hold any water while most nylon holsters have a foam middle that will function as a sponge if gotten wet.
Speaking of spray - it's your call to oil down/spray the gun for "added protection" prior to the trip, but remember to clean it up when you get home.
Remember to wear your PFD (and helmet if going near rocks).
stay safe.
Also, be sure to check the local laws on the waterway you will be using. If it is a river that borders MD, you CANNOT have a gun in your possession, because MD owns pretty much the entire Potomac.
If the river borders NC, you CANNOT have a loaded gun on a boat ramp if you put in or out in NC.
Just be sure you know exactly who "owns" the river you are on, and what the laws are with regards to portage and launches. These laws vary wildly from state-to-state...
Got a question. I am going rafting or canoeing soon and would like to carry down the river. Any suggestions for a waterproof gun container or holster????
My Glock had no problems with my 'river walking'.
If you have one that is more prone to get some Militec put a light coating on all the metal parts and then toss in to an over that had been preheated to 250 and turned off as you put the parts in it. Wait for oven to cool off and it will help protect from rust.