Well first of all, what the infectious agent actually is should be known. If multiple people are getting sick from swimming in the same area this generally sets of the alarm bells for public health people. I'm really surprised they haven't tested the sick people and the source of infection by now. So either it is a bacetrial or viral disease. If it is bacterial and you knew what sort of bacterium you were dealing with you could presumabley take antibiotics in a preventative manner.
I think that is a poor use of antibiotics, of course. If it is viral there isn't much you can do. I suppose it could also be protozoan, like giardia or something similar.
What you can do is simply not swim in that water. That seems like a pretty good idea. I'd ask whoever is giving this course why they don't have it in non-polluted water? I mean is there actually a need for you to swim in sewage contaminated water (which is likely what this is if you're getting diarrheal type infections from it)?
As for malaria, it was actually endemic in England way back in the day. In fact I think there were outbreaks as recently as WWII (from native malaria, there might be sporadic cases from people infected with malaria coming over). But it doesn't make you shit yourself like that.