Your C-41 final rinse should contain some product equivalent to photo-flo. Strictly speaking the final rinse is not C-41 so do check your workflow contains a proper final rinse. I think adding some photo-flo to your final rinse shouldn't give any damage.
Maybe your water is very hard. Maybe your final rinse is too diluted.
Personally I don't use a squeegee. I just extract the film from the tank, put it while in the reels inside the final rinse (this is considered wrong by some people, on the assumption that the final rinse contains some substance which stick to the plastic reels, my idea is that whatever substance can be removed and in any case I don't observe any deposit), extract it from the final rinse, open the reels, carefully get the film in my hands avoiding it to touch anything and avoiding to touch the images with my finger, and hang the film inside my drying cabinet using a weight to keep it properly extended.
Some people keep the film oblique so that the water slides more easily along one edge of the film and makes a drop on one of the bottom corner. It's done especially with plane film probably, which is easy to hang by one corner. I don't have enough room in my drying cabinet to keep the roll film oblique but observe no problems in the final result.
Before scanning I use air (a blower brush, take the brush away and only use the blower) and blow air on both sides. Works a lot. I also scan with ICE at minimum level (reduction of dust artifacts with automatic reconstruction of nearby zones). I observe no dust whatsoever on my scans.
The back of the film can be cleaned with most everything, even denaturated alcohol on some cotton, the emulsion side is trickier, in those rare occurrences when I had to clean it I use a product called PEC-12 with some specific little towels, PEC-PADS. It works especially well with finger marks, I have no idea if it is effective with water marks.
Personally I would try to dissolve water marks by re-immersing the film into final rinse and hanging it up again, hopefully the water will dissolve the water mark on the film. That would also take obstinate dust particles away hopefully.
If you have a shower with cabinet, or a small shower room, a good way to dry your film away from dust is to let hot water run until the room is full of vapour, then wait for the vapour to sit (it will bring down all dust particle in the air), hang your film, close the cabinet, exit the bathroom, close the door, don't enter in the bathroom until the film is dry. Remaining the bathroom stirs air which stirs dust which sticks on your film.