The longfin tilapia (Oreochromis macrochir) was introduced into Lake Alaotra from the mainland in 1954 and proliferated quickly.

These reedbeds provide the sole habitat of the endemic Alaotra gentle lemur (Hapalemur griseus alaotrensis).

The Alaotra gentle lemur is now limited to only 220 km2 (85 sq mi) of remaining reedbeds, and in recent years, its population rapidly declined by 60%, from about 7,500 individuals in 1994 to 3,000 in 2001, mostly from habitat loss, but also from hunting by local villagers.

The lake is the type locality of the butterfly Artitropa alaotrana and an important but increasingly threatened habitat for waterbirds, including the endangered Meller's duck (Anas melleri).

The Madagascar pochard is now critically endangered and no longer found on the lake, although very small numbers exist elsewhere.