Llyn Padarn is a glacially formed lake. It is one of the largest natural lakes in Wales and is approximately 2 miles (3.2 km) long and at its deepest point is 94 feet (29 m) deep.

Llyn Padarn is home to a population of Arctic charr, a rare fish that has become isolated in some lakes after the last Ice Age ended. The Welsh populations of charr are a distinct race and the population at Padarn is genetically different from those in Llyn Cwellyn and Llyn Bodlyn. Spawning in Llyn Padarn occurs locally in shallow, marginal waters, notably along Afon y Bala.

Llyn Padarn is home to two notable species of aquatic plant, floating water-plantain (Luronium natans) and small quillwort (Isoetes echinospora).

Otters and small numbers of wildfowl frequent the lake.

At its outflow from Llyn Padarn, the Afon Rhythallt, is one of the most important spawning sites for salmon and sea- trout in north Gwynedd.

Llyn Padarn is of national geological importance because the 600m-long section located alongside the Llanberis Lake Railway exposes a thick sequence of volcanic and sedimentary rocks of Cambrian age.