Much Wenlock Parish Council said removal of minerals as part of the work will have "serious consequences" for the water ecosystem in the Gorge.
Power station developer Harworth said it had carefully developed its plans, but that it was important to get them right at this stage.
The company urged everybody to have their say on the plans ahead of the deadline on March 20.
In its objection, Much Wenlock Parish Council said: "Flooding is of considerable concerns, both for local residents and indeed visitors on whom we rely to support our communities.
"Removal of minerals could result in stabilisation issues and have serious consequences for groundwater reserves and the whole water ecosystem. This cannot in our view be allowed to be disturbed so close to an area so vulnerable to flood dangers and should not in any way be permitted."
Due to flooding, the opportunity for the public to have their say on the plans has been extended until March 20.
Iain Thomson, of Harworth, said: "We agreed a 56-day public consultation with Telford and Shropshire Councils at the very outset, owing to significant local interest in the application. If any locals haven't looked over the plans thus far, we strongly urge them to do so before deadline.
"The recent floods have been devastating and shows just how important it is for us to get our plans right at this stage. We've been very careful with which parts of the site have been suggested for development and we want to reassure residents that we will continue to be moving forward."
Ironbridge was hit hard by floods over the last couple of weeks, with much of The Wharfage being closed off and evacuated.
Shaun Davies, leader of Telford & Wrekin Council, said Ironbridge needed £50 million permanent flood barriers.
But Environment Agency spokesman Nick Green said permanent barriers would be impractical because of planning issues in the Gorge, which is a World Heritage Site.