They may have had to clear some of the debris to get at the core drilling sites. In any case, whatever the beavers did, the constructed storm water treatment wetland wasn't working as designed. Walking around, I am not even sure it can -- it isn't evident where the water source for it is, beyond seepage up. Perhaps the lagoon 'silted' too much from organic decay over the years and no longer effectively is connected to the river at the 'source' end of the lagoon.
The lagoon is nice and all, but it is a built environment and we have to remember that. The natural environment there is a gravel bar.