Nahuel Huapi’s flora and fauna resemble those of Parque Nacional Lanín to the north and Parque Nacional Los Alerces to the south, but differ in some respects. There are three principal ecosystems: the easterly Patagonian steppe, the Andean-Patagonian forest, and the high Andes above 1,600 meters, which consists of low shrubs and sparse grasses adapted to cold, wind, and snow.

Guanacos graze the semiarid steppe grasslands, stalked by foxes and even pumas, while raptors like the cinereous harrier and American kestrel patrol the skies. Toward the west, open woodlands of coniferous cypress, ñire (southern false beech) and maitén stand among rocky soils.

Farther west, at slightly higher altitudes, dense false beech forests of coihue, lenga, and ñire cover the slopes, while the shoreline and stream banks burst with a flowering understory of notro and climbing vines like mutisia with clusters of the cinnamon-barked arrayán.

Near Puerto Blest, rainfall up to 4,000 millimeters per annum supports a humid Valdivian forest of Guaiteca cypress, Podocarpus, and tree ferns. Nahuel Huapi, though, lacks Lanín’s monkey puzzle forests, and the more southerly alerce tree is less abundant than in Chubut Province.

Sightings of the huemul (Andean deer) and the pudú miniature deer are rare here. Other mammals include the carnivorous huillín (otter) and the tuco-tuco, an endemic ground squirrel–like rodent.

Normally oceangoing, the king cormorant has a colony along Lago Nahuel Huapi, where the kelp gull often trails the boats that sail the lake. Nahuel Huapi, its tributary streams, and other lakes teem with trout and other fish.