The Government has acknowledged that biodiversity is an integral part of natural beauty and nature conservation is therefore a high level objective of designation. The Nidderdale AONB is host to a varied mosaic of upland habitats that support a diversity of wildlife species. 

Many of the AONB's wildlife resources are of national or international importance. 25,000 hectares of heather moor contained in the East and West Nidderdale Moors Site of Special Scientific Interest form part of the North Pennines Special Protection Area designated under the EC's Birds Directive. This same area is also a candidate Special Area of Conservation under the EC's Habitats Directive. 

The AONB encompasses 13 Sites of Special Scientific Interest (SSSI) including calcareous grassland and woodland that are designated under provisions contained in the 1981 Wildlife and Countryside Act.  Three SSSI's in the AONB have been designated because of their geological importance.  There are 48 (non-statutory) Sites of Importance for Nature Conservation (SINCs) in the AONB that are referred to in Harrogate Borough Council's District Local Plan.

Responsibility for the management of these sites rests with private landowners who receive advice and assistance from several government agencies including Natural England and the Environment Agency. Public access to these sites, whether SPA, SAC, SSSI or SINC is via public rights of way or the new right of access to open country only. There is no de facto right of access to any of the sites referred to here by virtue of their nature conservation status.