A wildlife charity fears it could lose a funding grant after a burst pipe prevented vital conservation work.
It is the fourth time Long Mead Local Wildlife Site, at Swinford in Oxfordshire, has been flooded because of a mains failure.
Although the meadow by the River Thames naturally floods in the winter, standing water at this time of year can cause damage to the rare habitat.
Thames Water said the latest leak had been fixed and it remained committed to protecting local wildlife sites.
“It’s already starting to stagnate, so that’s serious,” said Catriona Bass, director of the Long Mead Foundation.
“Floodplain meadows are used to flooding in winter when the plants are dormant.
“These meadows don’t flood typically in summer and when they do it’s a disaster because the plants are growing – so it kills off the plants.”
The site is central to a restoration programme that aims to boost this type of specialist habitat across the county.
There are only four square miles in total of floodplain meadow in the country – the equivalent in size to Heathrow Airport.
The rare habitat is home to deep-rooting wild flowers and grasses like great burnet and devil’s-bit scabious.
