There are several Nature Reserves and related protected nature conservation areas owned, operated and managed by a range of organisations across the County Borough containing a range of different habitats, species and designations. Nature Reserves include:

• Cwm Taf Fechan Local Nature Reserve/SSSI – South & West Wales Wildlife Trust/Merthyr Tydfil CBC/Private
• Cwm Glo a Glyndyrus SSSI - Private
• Cilsanws Nature Reserve – Merthyr Tydfil & District Naturalists Society
• Webber’s Pond and Jack’s Wood Nature Reserve - Merthyr Tydfil & District Naturalists Society
• Penmoelallt SSSI  Community Woodland - Merthyr Tydfil & District Naturalists Society/Forestry Commission Wales
• Pontygwaith Nature Reserve – Private/Merthyr Tydfil Angling Association
• Darren Fach Nature Reserve SSSI – Private/Brecknock Wildlife Trust