The ship canal's actually not bad in terms of wildlife - I saw six kingfishers on a recent transit, along with quite a few gadwall and shelduck amongst various other birds breeding there (which all go to suggest a not-unhealthy population of fish, plants and bugs). The canal also runs right along the edge of/discharges into the Mersey Estuary which is designated as being of international importance for conservation (Special Protection Area and Ramsar site), particularly for waterbirds. It's likely that a number of the associated birds also use the ship canal (e.g. shelduck) and so it would be classed as Functionally Linked, so negative impacts on the canal might be considered to be affecting the designated sites. They probably ought to be undertaking a Habitats Regulations Assessment (HRA) if they haven't already, and I do wonder whether that would be able to conclude no impact.
All that to say, pumping sh**e into a waterway is bad for the wildlife and should drop the perpetrator into hot water, legally speaking. But then they've been allowed to do it all over, so who knows.