The lake is of glacial origins, and its morphology derives from over-excavation phenomena which led to the formation of the lake basin and of the surrounding hillocks. The rocky substratum mainly consists of prasinite and by limited outcrops of serpentinite, especially on the hillocks surrounding the lake. Lago di Villa is very interesting for its geographical position. It lies in an area characterized by the presence of low mountains and habitats which are rare or unique in Valle d'Aosta. The vegetation is characterized by Scotch pines, durmusts, and chestnuts. Woods also alternate with some pasturelands which are running wild. The lake houses the only site of Nimphaea alba in Valle d'Aosta.
The priority habitat "Semi-natural dry grasslands on calcareous substratum (Festuco Brometalia) with wonderful orchid bloomings" lies in the dry meadows of the north-west.
The reserve represents a good site for the reproduction of toads, pool frogs, and recently of little grebes, birds typical of the wetlands.
The wildlife of the Nature Reserve mainly consists of Amphibians and Reptiles. Together with the Common Toad (Bufo bufo), to which Villa lake represents the main reproductive place in the region, there are the Edible frog (Rana esculenta) and the moor frog (Rana agilis). The reptiles are the Common wall lizard (Podarcis muralis), the Western whip snake (Coluber viridiflavus), and the Grass snake (Natrix natrix).
The fish fauna is represented by Cyprinids.