Naturalists were originally drawn to Wicken because of its species richness and the presence of rarities. The Fen has therefore received a great deal of recording effort and huge species lists have accumulated. Many nationally rare species have been recorded.

Wicken Fen has been designated as a:

• National Nature Reserve
• Site of Special Scientific Interest under the Wildlife and Countryside Act 1981.
• Special Area of Conservation under the EU Habitats Directive.
• Wetland protected under the international Ramsar Convention.

There is no higher recognition of ecological importance. These designations have been principally made on account of the open Fen habitats such as sedge beds, reed communities and Fen meadows. Aquatic habitats such as the dykes and pools are also very important. Dryer grassland and woodland also add diversity to the site but in the case of woodland, its expansion has often been at the expense of more valuable open Fen habitats.

The Fen has a prodigious list of rare species. It was established as a nature reserve because of its invertebrate interest. Nearly 5,000 species have so far been identified on the Fen, including more than 121 that are included in the Red Data Book of rare invertebrates. All of the species will benefit from habitat restoration work.