The island is of geological interest with pillow lava, jasper formations and aeolian sand deposits.

The island forms part of the National Nature Reserve of Newborough Warren which includes the extensive and floristically rich sand dune system.

In respect of the site having 'spectacular, accessible and well-preserved exposures of late Neoproterozoic-Cambrian mélange with more than 200 years of study', the International Union of Geological Sciences (IUGS) included the 'Ynys Llanddwyn late Neoproterozoic-Cambrian Mélange' in its assemblage of 100 'geological heritage sites' around the world in a listing published in October 2022.

[3] Newborough National Nature Reserve & Forest, of which Ynys Llanddwyn is part, received 478,204 visitors in 2018.

[4] There are more than 10 miles (16 km) of footpaths crossing Ynys Llanddwyn and Newborough Warren, including the Anglesey Coastal Path, and it is a very popular place to visit.