There's Several hypotheses must be observed in this situation ,and then upto start discussed it one by one:
1-The first one: the poisoning, the question must be is the fishes and the organisms in the river have the same mortality as they have in the cages??
And are the fishes and organisms at the top of the river have same mortality as the first place ? and must be concern if there is any facilities near by the poisoned area such as a power station or degassing station or any sources of pollution .
2-The other hypothesis is if there's any viral or bacterial diseases effected this area ,and did all of the fishes and organisms in the cages and the river were infected ?
3-The third hypotheses is: did you care about the specified distances that must be existed between the cages ?
4-The fourth one and the more important condition is the density per square meter which depend on the quality of the water and the speed of the flow.
Then when you analyze these hypotheses, you can get the right reasons for this phenomena.