A map released by the Environment Agency highlighting 'severely affected' areas runs an almost identical course to the proposed HS2 route through Leeds, raising questions about the feasibility of the £55.7bn pound project.
Most of the proposed land for development towards Leeds Station was under water this weekend as the river overflowed.
The line will pass through 45 miles of Staffordshire with campaigners warning some of the land floods.
UKIP MEP Mike Hookem said: "Flood defences are not something that the government can palm off on charities and communities like many other aspects of life in Britain today.
"So rather than pouring billions of pounds into vanity projects such as HS2; while at the same time cutting the flood defence budget - as it did in the recent spending review - the government must get its priorities right and make protecting the homes and businesses of hundreds of thousands of people from flooding an absolute priority.
"While flood defences are dour in comparison to the sexy sound bites used to promote HS2, each year we are seeing more and more homes and businesses blighted with the misery of flooding in the north of England.
"HS2 is not a magic bullet to bridge the North-South divide and the destruction of property and peoples livelihoods though repeated failures to tackle flooding is doing nothing more than further exacerbating the problem."