Four tortoise species occur within the area. Of these, the most likely to be seen are the marsh terrapin and the large leopard tortoise. The tent tortoise, a Cape endemic, is occasionally seen in the drier western and north-western areas while the angulate tortoise is a common resident of the southern part of the Baviaans.
Although the majority of the 24 snake species found in the area have a wide distribution range, 4 of these are South African endemics.
The snakes most likely to be seen are Cape cobra, puffadder, boomslang, rhombic skaapsteker, Karoo and montane grass snakes and the brown water snake. The Cape cobra and puff adder, are generally regarded as the two most dangerous.
The lizard fauna of the wilderness area is remarkable. Of the 28 species present, two newly discovered species, a dwarf chameleon Bradypodion sp. and a flat gecko Afroedura sp. are endemic to the area. A further 7 species are Cape endemics and 7 others are South African endemics!
Most of these occur in the mountainous parts. In summer the Nile monitor is commonly seen near water.
The ubiquitous Southern rock agama can be found almost wherever there are rocks and sunshine.
The rivers flowing through the area support a diverse indigenous fish fauna - fifteen species are known to occur here, of which three are endemics to the rivers of the Cape. Little red-finned minnows will swim up to nibble one’s feet if dangled in the water.
There are around 80 subspecies of them in the Baviaanskloof streams, each group cut off from the rest and developing seperately, like Darwin's finches.