Typical misleading reporting from the Daily Wail, I see.
The European Water Framework Directive obliges governments to ensure that the impact of any structural measures (such as dredging) are assessed and o prohibit any such measures that might, for example, adversely impact the quality of drinking water supplies. (That sounds like a good idea to me. I'd rather that nitrates, from fields alongside river courses, didn't end up in my drinking water!)
However the Daily Wail conveniently forgets to mention the EU Floods Directive 2007, which is European legislation which "requires Member States to assess if all water courses and coast lines are at risk from flooding, to map the flood extent and assets and humans at risk in these areas and to take adequate and coordinated measures to reduce this flood risk".
So EU legislation is actually demanding that governments act to reduce the risk of flooding, rather than preventing them from doing so.