Devon rescue group Prickles in a Pickle said it had received a surge of reports of hedgehogs washed from nests in the Plymouth, Kingsbridge, Ivybridge and Dartmouth areas.
Co-founder Judy Thompson said this winter had been “hard hitting” for the animals.
“They have been flooded out of their homes and at this time of year, food is scarce,” she said.
“If they’re underweight, or they’ve struggled into the winter in the first place, this is a double hard hit for them.”
Some hedgehogs arriving at the rescue centre felt like “little empty bags of prickles and very, very slim” due to dehydration, Thompson said.
She said they were unable to safely drink the flood water because they could be swept away and their main food source, worms, have been flattened or dried out by the rain.
Thompson said increasing development on and near floodplains was also cutting off wildlife refuges: “Building sites are stealing habitats, leaving wildlife with nowhere to go.
“There needs to be more natural management of floodplains and drainage.”
The European hedgehog is protected under the Wildlife and Countryside Act 1981 and is classified as “vulnerable to extinction” on the IUCN Red List for British Mammals, external.
Their numbers have fallen below one million in the UK which is down by 30% in more than 10 years, Devon Wildlife Trust said.
Thompson said: “We can’t afford to lose them as fast as we are… I for one don’t want to see them disappear.”