The Makgadikgadi Pans are perhaps best known for their birdlife; specifically the great concentration of waterbirds in the Nata River delta after good rains (December–April). In good years, tens of thousands of flamingos, both lesser and greater, arrive to breed, visible from the air as a pink shimmer across the surface of the lake. They are sustained by a rich soup of algae – and brine shrimps, whose eggs had lain dormant in the baked clay of the pan surface throughout the dry season.

This gathering represents the largest breeding flamingo population in southern Africa, and can peak at over 100,000 birds. However it is a very unpredictable phenomenon. Even after good rains the flamingos have a life-and-death race against time to breed before the waters dry up, and they may not return again for years. In 1976, over 5,000 young flamingos, still unable to fly, were observed from the air trekking en masse across the barren pans in search of new water when their breeding shallows evaporated. What became of them is not recorded.

The flamingos can best be seen in the Nata Bird Sanctuary. Here, when the flood is full, you will also find pelicans (both white and pink-backed), herons and egrets, cormorants and darters, waders (including avocet, blackwinged stilt, blacksmith plover, wood sandpiper and ruff), black-necked grebe, red-knobbed coot, and ducks (including red-billed teal and white-faced duck). Other species more typical of the Okavango floodplains also occur at this time, including fish eagles, saddle-billed storks and, occasionally, wattled cranes. The reedbeds themselves provide a breeding habitat for weavers, bishops and reed warblers.

The open grasslands surrounding the pans are home to many typical Kalahari ground-nesting birds, including ostriches, which are sometimes seen far out on the pans themselves, kori bustards and secretary birds. Some smaller species, including capped wheatear and ant-eating chat, take this a stage further by nesting, like rodents, in underground burrows. All four of southern Africa's sandgrouse Namaqua, Burchell's, double-banded and yellow-throated) occur around the pans. These delicately plumaged birds are most often seen in the evening, flying rapidly towards a waterhole with rippling calls. Males will waddle in to immerse their absorbent belly feathers and carry water back many kilometres to their young on the nest.

More conspicuous by day is the boldly-marked male white-quilled korhaan, who calls with a noisy 'karak karak karak' as he takes off and circles slowly in territorial display, before fluttering to the ground with yellow legs dangling. Like all korhaans, the brooding female relies on her cryptic camouflage to remain hidden. Another common species, the double-banded courser, is superbly adapted to withstand the harsh conditions of the pans. It does not need any drinking water, and can survive extreme overheating while protecting its single egg from the fierce Makgadikgadi sun.

In this largely featureless habitat, any point of elevation can prove a good spot for birds. The baobabs on Kubu island provide roosting and nesting sites for barn owls and rollers (both lilac-breasted and purple). Many tall stands of date palms harbour breeding palm swifts, and the occasional pair of red-necked falcons. Isolated thorn trees support the massive untidy nests of secretary birds or vultures (both white-backed and lappet-faced).

The acacia woodland holds a wide selection of birds typical of this habitat across the region. Red-billed francolin, white-browed robin and violet-eared waxbill forage low down in the thickets, while lilac-breasted roller and long-tailed shrike perch more conspicuously in the taller acacias. Bateleurs and martial eagles patrol the skies, and a host of bulbuls, babblers, hornbills, barbets, sunbirds, flycatchers and others occupy the niches in between.

The area around Nata Lodge is particularly rich in woodland species. In summer, migrant raptors such as steppe buzzard, western red-footed kestrel and yellow-billed kite join resident predators such as greater kestrel, pale chanting goshawk and marsh owl, and after good rains, Montagu's and pallid harriers may be seen quartering the grasslands in drifting, elegant flight.

Other common summer migrants include white stork, red-backed and lesser grey shrikes and European and carmine bee-eaters, while seed eaters such as red-billed quelea and black-eared finchlark arrive to breed in large numbers, taking advantage of the seasonally abundant grass seeds.

Flamingoes

Of the world's half-dozen or so species of flamingo, two are found within southern Africa: the greater, Phoenicopterus ruber, and the lesser, Phoenicopterus minor. Both species have wide distributions, from southern Africa north into East Africa and the Red Sea, and are highly nomadic in their habits.

Flamingos are usually found wading in large areas of shallow saline water where they filter feed by holding their specially adapted beaks upside down in the water. The lesser flamingo will walk or swim whilst swinging its head from side to side, mainly taking blue-green algae from the surface of the water. The larger greater flamingo will hold its head submerged while filtering out small organisms (detritus and algae), even stirring the mud with its feet to help the process. Both species are very gregarious and flocks can have millions of birds, though a few hundred is more common.

Only occasionally do flamingos breed in southern Africa, choosing the Makgadikgadi Pans, Namibia's Etosha Pan, or even Lake Ngami. When the conditions are right (usually March to June, following the rains) both species build low mud cones in the water and lay one (or rarely two) eggs in a small hollow on the top. These are then incubated by both parents for about a month, until they hatch. After a further week the young birds flock together and start to forage with their parents. Some ten weeks later the young can fly and fend for themselves.

During this time the young are very susceptible to the shallow water in the pans drying out. In 1969, a rescue operation was mounted in Namibia when the main Etosha Pan dried out, necessitating the moving of thousands of chicks to nearby Fisher's Pan – which was still covered in water.

The best way to tell the two species apart is by their beaks: that of the greater flamingo is almost white with a black tip, while the lesser flamingo has a uniformly dark beak. If you are further away then the body of the greater will appear white, while that of the lesser looks smaller and more pink. The best place to see them in Botswana is certainly Sua Pan – although even there they will only appear if the rains have filled some of the pan.