So it is a pretty different situation compared to if they had been removing trash by hand, which is much less likely to cause unforseen harm. The heavy machinery will compact soil, potentially leak oil/fuel. The mechanized digging of the stream bed could disturb benthic species and stir up silt that could have negative impacts further downstream.

Without appropriate precautions, this fellow could easily cause more harm to the ecosystem, which is one of the reasons that this is not and should not be legal. It sounds like this group did do some background work to try to make sure they were doing the right thing, but I don't think it should be open season for anyone with a backhoe to dredge a local body of water based on their own judgement.