The site contains a range of habitats including spring-fed lowland fen, dominated by rushes and sedges, a variety of ponds, and wet woodland with small representations of lowland calcareous grassland, wood pasture and parkland. Lye Valley has one of the best examples in the country of a calcareous valley fen, a nationally rare habitat. The plant and animal species of the Lye Valley fen are thought to have lived there since they colonised the spring areas after the retreat of the last ice age between eight and ten thousand years ago.
The site has been studied by botanists since the 17th century and attracted particular interest in the Victorian era. More than 300 species of vascular plants have been recorded in the area, though some of them have not been found in recent years. Rare plants include grass-of-Parnassus and marsh helleborine orchid, which are on the Red List of Threatened Species compiled by the International Union for the Conservation of Nature (IUCN).[5]