Verlorenvlei supports more than 189 bird species, of which 75 are waterbirds. The wetland occasionally hosts more than 4 000 birds; the highest number recorded in a single count was 11 891, according to the data from counts undertaken by CapeNature since 1990. At least 26% of the Western Cape’s Great White Pelican Pelecanus onocrotalus population congregates at this site at times. Greater Flamingo Phoenicopterus roseus and Lesser Flamingo Phoeniconaias minor also occur here occasionally, when conditions at Rocher Pan (35 km south) or Wadrifsoutpan (13 km north) are unsuitable or water levels in the lake are very low, as occurred in the 2004–2005 season. Relatively large numbers of Little Bittern Ixobrychus minutus and Caspian Tern Sterna caspia occur regularly in the wetland.

Historically an important moulting ground and summer refuge for Anatidae, the area supported large numbers of Yellow-billed Duck Anas undulata, Cape Shoveler A. smithii and South African Shelduck Tadorna cana. However, many of these species have declined over the past decades, as data from CapeNature illustrate. Large numbers of Great Crested Grebe Podiceps cristatus, Red-knobbed Coot Fulica cristata and White-breasted Cormorant Phalacrocorax lucidus can also be found at this wetland. There is a high density of African Marsh Harrier Circus ranivorus, which forages over the marsh and reedbed areas. Black Stork Ciconia nigra breeding in the Olifantsrivierberge and Swartberge to the east and Piketberge to the south very occasionally forages in the vlei. The site also holds 4–5 pairs of African Fish Eagle Haliaeetus vocifer, and Verreauxs’ Eagle Aquila verreauxii occurs on the cliffs around the vlei.

African Black Oystercatcher Haematopus moquini and Chestnut-banded Plover Charadrius pallidus are recorded at the estuary mouth from time to time. The palustrine habitats are diverse and rich and hold populations of secretive Rallidae such as African Rail Rallus caerulescens and Baillon’s Crake Porzana pusilla. Red-chested Flufftail Sarothrura rufa may occur, but has not been confirmed. Rallid species are particularly abundant between Matjiesgoeddrif and Redelinghuys, where the composition and structure of the palustrine vegetation are diverse and the area has extensive and excellent habitat for them and for waders. The diverse ecotonal terrestrial vegetation around Verlorenvlei’s fringes supports several restricted-range and biome-restricted assemblage species. In recent years, a pair of Goliath Herons seems to have been resident in the area and may be breeding.