Since the reason for not swimming in the Seine was sewage, a "stomach bug" is exactly the problem you'd expect to develop after swimming in it. To rule the water out, you'd need evidence that, say, the guy ate at a restaurant with several other people who didn't go swimming, and they got sick too.
Why not just compare the incidence of sickness at the swimming event vs other triathlon swimming events and see if 2(or whatever the number of competitors affected was) is abnormal and work from there?
That would be an approach to the question of "is the Seine dirtier than other triathlon events?", but it wouldn't address the question of "how did this guy get sick?"
i cannot find current data, but france had more food poinoning case than the us about 20 years ago (that is not per capita, that is total) thus it something they ate is not unlikely
