The estuary is important for the recruitment of fish such as leervis, steenbras, two species of stumpnose and a number of other species.
The surrounding wetland is an important habitat for birds and has 166 species on its official list. It is also a vital habitat for amphibians and about 20 species of reptile such as the angulate tortoise, marsh terrapin, mole snake and brown water snake. Porcupines, grysbok, otters and mongoose can also occasionally be spotted in the reserve.
Amphibians
There are 6 species of amphibians recorded in Zandvlei. One of these, the Western Leopard Toad is endangered and is a Red Data Species. It does however have good distribution throughout the estuary.
Birds
Of the 166 different birds recorded for the Reserve 6 are Red Data Species. These are the Eastern White Pelican, Little Bittern, Greater Flamingo, African Marsh Harrier, Perigrine Falcon and the Caspian Tern.
Fish
Thirty four species of fish have been recorder in the estuary. Two of these, the White Steenbras and the Cape Galaxia are Red Data Species.
Insects
30 different insects have been collected within the Reserve.
Mammals
There are 22 mammals recorded in the Reserve, the most recent being the Brants Climbing Mouse which was recorded in 2005. The Cape Clawless Otter, Porcupine, Grysbok and Water Mongoose are fairly common.
Reptiles
The following reptiles have been recorded: 9 species of snake, 7 lizards, 1 tortoise, 1 terrapin and 1 juvenile turtle. Two records of yearling Loggerhead turtles have been made.
