As with everything else, it depends. What is the river polluted with? And, were the logs green, or long dead when they went into the river?
A fresh, green log will absorb very little external moisture, whereas an old, half decayed log will absorb like a sponge. Depending on what kind of trees they were, a good percentage of whatever they absorbed would first be absorbed into the more porous bark than into harder wood.
If you are concerned, a tool such as a draw plane, or spoke shave could be used to remove most of the bark. Since the river is a source of drinking water in the region, the pollutants are probably not that serious. Check with the water treatment plants for data on what pollutants you are dealing with. That data
should be a part of the public record.
Good luck. Every disaster brings small benefits as well.