I'd be more worried about disease propagation. Would need to be self-cleaning, methinks .. super-clean the pipe in between fishy-pilot takeoff with a super-steaming? Hmm .. Combine the two, and we've got lunch. :)
It seems unlikely that they're going to be exposed to anything in the tube that they're not already exposed to when they congregate together at the bottom of a dam (or a natural waterfall). They can get pretty packed..
As another poster noted, at this stage they're not likely to live long enough to develop most diseases.