It has nothing to do with the EA unless they need to enforce or regulate something eg, inappropriate discharge from an unlicensed facility etc. Any complaints would need to be addressed by the water board in question (who will be licensed)and unless there has been a discharge deemed to be unfit for whatever reason (happens regularly) then the EA wouldnt havevto step in. They provide the regulations that people/industries/local authorities/farms/petrol stations etc have to abide by.
Most rivers will have sewage impact during rainy periods, that is how it works when there is too greater volume of water to be processed at the works it will over flow. Sounds as though the lady in the article is getting the rough end of the stick though, I'm sure she could make a complaint via local EHO (environmental health offucer) at the council, not the EA.
As for what they have done .... regulate water quality, provide fish stocking programmes, regulate discharges, monitor all sorts of environmental issues. On the downside , cut backs, reduction in staff, lack of funding will all play a part in how they operate in the future