I've been having similar problems with my water. No matter what I do, it invariably becomes septic. My first river and subsequently the channel i sent to my fort spontaneously became stagnant, and waterwheels refused to work anywhere along my channel. After finding out that stagnant water apparently irradiates everything it touches with horrible stagnation rays, I created a new channel, involving pumps and virginal mined-out corridors. The water came through the pump and remained water for approximately eight tiles, wherein it decided unpotable is the new fresh and randomly became garbage water. Oddly, the waterwheels in this section started chugging along fine. Finally, i decided to forget the river and see if i could have some fun mining out an aquifer as a freshwater source. Since this whole ordeal was simply to create a fabulous multi-waterfall in the dining room, i used a series of pumps to move the aquifer's precious clean water to the proper place. Amazingly, it made it all the way up a 3 level pump stack (clean the whole way, mind you) before deciding that the water that would ultimately rain upon my dwarves would be fabulously horrible.
Would constructed walls and floors actually help, as others have claimed? Because the problem seems to stem from the existence of several 7 depth tiles in a row, as the water remains water until whatever passage it is moving through starts filling up.
Also, im in 34.02, and this particular version of DFHack doesn't seem to recognize "wclean". Took me a minute to notice the interceding step. DFhack -> liquids -> wclean. Did the trick. Have to see if the rainy season pollutes the world again.