The Warren is bounded by two rivers - the Afon Braint to the southeast, the Afon Cefni to the northwest - and includes Llanddwyn Bay and Malltraeth Bay, divided by the slim finger of Ynys Llanddwyn pointing south. What makes the dune system so internationally important is the combination of active dunes (still moving, still being shaped by wind) and fixed dunes (stable enough to support diverse plant communities), with freshwater pools called dune slacks in between. Many fixed dunes are now buried under the forest plantation. The freshwater pools and the salt marshes that flank them are wintering grounds for waders and wildfowl - the mudflats regularly support over one per cent of the British population of pintail, an elegant long-tailed duck. On Ynys yr Adar, a tiny rocky islet near Ynys Llanddwyn, more than one per cent of the entire British breeding population of cormorant nests every year.

By the late 1970s the forest was raising concerns. Water levels in the woodland and in the neighbouring dune systems were falling. Winter flooding was shallower than it had been. Dune slack pools - the small freshwater hollows where rare orchids and amphibians breed - were drying out earlier each summer. Was the forest itself to blame? Pine plantations transpire heavy quantities of water, and afforesting a previously open dune system might have raised the local evaporation demand enough to lower the water table. Other UK Atlantic dune systems were also reporting low water tables in the same period, due partly to low winter rainfall, so the forest could not be wholly blamed. Still, clearings were cut, and the forest bordering the open Warren was heavily thinned. Proposals in 2004 to remove large parts of the plantation outright met fierce local resistance, and in 2008 a public consultation was held. The Forestry Commission and Natural Resources Wales now manage the forest in compromise: kept, but pruned for the wetland's sake.

The plant list reads like a botanist's wishlist. The endemic dune helleborine Epipactis dunensis grows here. So does the dwarf adder's tongue Ophioglossum azoricum. The nationally rare shore dock Rumex rupestris finds toeholds among the strand line. On Llanddwyn Island the nationally rare golden hair lichen Teloschistes flavicans was rediscovered in recent years - its bright yellow tufts catching the light on coastal rocks. The dune slacks host marsh orchids, butterwort, grass-of-Parnassus, even the strange parasitic yellow bird's-nest. Round-leaved wintergreen has spread across much of the dune system in the past decade. Common dune flowers - dune pansies, sea spurge, sand cat's-tail - cover the slopes wherever they have a chance. The fauna keeps pace with the flora: red squirrels in the forest, herring gulls, oystercatchers, lapwings, curlew, skylarks, meadow pipits, toads, lizards, and a wealth of invertebrates that supports everything above them. The Warren featured on the BBC's Autumnwatch in November 2008 in a segment about the importance of ravens to the local food web.

At the extreme southern tip of the Warren is Abermenai Point, a low sandy spit reaching out into the strait. It is the probable location of the earliest ferry crossing over the Menai Strait to the Welsh mainland - the place where, for a thousand years before any bridge existed, travellers shouted across the water for a boatman to row them over. The same spot is now part of the Anglesey Coastal Path, a 200-kilometre walking route that loops the entire island. To walk south through Newborough Forest, then west across the open Warren, then onto the causeway out to Ynys Llanddwyn at low tide, is to pass through one of the most layered landscapes in Wales: a planted woodland over engineered dunes over older dunes over a medieval planted town over a Welsh prince's court over Iron Age earthworks, with Snowdon visible across the strait the entire way.