To further clarify: the transgression, according to the Guardian, wasn't just removing waste, but the fact that "Powesland [...] organised a team of volunteers to tackle the removal of litter, weed and silt from a section of the River Roding", and they collectively "removed 200 bags of rubbish, branches and silt", which goes beyond just picking up trash.

The EA [Environmental Agency] alleges dredging has been carried out and waste has been left on site within the flood plain, constituting a flood risk activity under the regulations that would have required an environmental permit.

Dredging is the act of removing material from the water environment, here presumably from the riverbed, which is a tad more involved than just picking up pieces of trash and might have ecological knock-on effects. I find it perfectly justified that the Environmental Agency would want to be involved in the decision to take such steps.

The only real scandal is this guy having petitioned the Agency about the trash problem for years without success. That they'd now get pissed when someone takes the matter into his own hands is understandable, but might just be the only way to get them to care about the issue.