Local authorities from lots of EU regions generally avoid measuring water quality after rainy days because raw sewage is still often dumped under those conditions.
Even in Basel, where the Rheine is really clean, authorities sometimes advise not to swim.
As expensive as this project is, separating the storm drains from the sewage lines (https://en.wikipedia.org/wiki/Combined_sewer) in an existing system is much more costly.
There was a ton of work done to reduce the amount of water ending up in the sewer during storms followed by some large infrastructure improvements to improve the carrying capacity of the sewer itself.
https://www.bbc.com/news/science-environment-68464798
I think there's a B1M episode on Youtube that has a good overview.
Back in my day we'd have river fires that burned 50' high and burn bridges.
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).
Also Burgundy is just another part of France which is in the EU, so not really sure what you mean.