An important part of the pollution in the Seine is from Paris itself. Due to being an old city, the sewer system and the flood water system (i.e rain) goes through mostly the same tubes and are dump directly in the Seine. This leads to the river being full of biological contaminent, a.k.a, shit.

A lot of effort was done to remediate this very old issue, with a very big push before the Olympics games (but improvement to the sewage system has been going on for years).

The seine, burgundy and paris are all part of EU.

Turns out you can dump raw sewage in rivers at any point along them, not just the source.

Also Burgundy is just another part of France which is in the EU, so not really sure what you mean.