Unless something major has been changed with contaminant spreads since last I worked with them (which, admittedly, was quite a while ago), then being clothed or naked will make no difference if you're swimming in a contaminated flow. Flows will tag EVERY bodypart AND the clothing on top of it with every contaminant that the tile contains. Clothes can only protect you when walking over puddles/pools of contaminants on "dry" ground.
I'd say the safest bet would be to make sure you have wide channels for the water to move through. Narrow channels increase the risk that contaminants will get "stuck" on the walls rather than spreading to and being multiplied by adjacent flow tiles. You'd still need some sort of contact poison though, and there aren't many particularly useful ones that are readily available. If you just want to annoy/mildly inconvenience someone, cave blobs automatically generate a mild irritant on their skin, so pitting one into a pool of water will spread things around very quickly. I believe cave floaters can also muck up a water supply, but only when they're actively attacking something.
One particular benefit to water-borne contaminants is that they will cover every part of a victim's body with the stuff, so long as it isn't an internal organ. This includes stuff that normally wouldn't be at risk in a combat scenario, such as the eyes, mouth and throat. But in order to infect someone, you'd have to get them to actually be located inside the flow in question, which makes it fairly tricky as a defense measure.