ily and Blossom are about to be toilet trained at Taronga zoo. The two young sugar gliders are curled up together inside a wooden box within a staff bathroom while trainer Suzie Lemon is trying to coax them out with the promise of a sugary, sap-like treat. Lily eventually emerges and promptly pees all over the floor but Lemon doesn’t seem to mind. After all, they’re not here for that kind of toilet training.

“We’re training them to glide over to us on cue to demonstrate their natural gliding behaviour,” Lemon explains. “We needed an enclosed space, somewhere with four solid walls, because in future they’re going to be doing this for education purposes in the new learning centre.

“These two are both young so they’ve got to build their confidence and learn how to aim.”

Lemon raises her palms to form a wide landing pad and beckons Lily over. When the marsupial takes off it spreads its limbs to reveal wing-like membranes before landing on Lemon’s wrists.

“They do a bit of head-bobbing in order to judge the distance before taking off,” she says, “but sometimes they overshoot.” And, evidently, sometimes they pick their own target, such as the nearest leg.

  • Sugar gliders Lily and Blossom learn how to glide with keeper Suzie Lemon inside a staff toilet at the zoo’s ‘backyard to bush’ section. Photographs by Jonny Weeks for the Guardian.

Sugar gliders are nocturnal by nature but many of the zoo’s approximately 4,000 inhabitants and 110 full-time keepers have been up since first light – long before the zoo’s gates opened to the general public.

Over at the pygmy hippo enclosure, four-month-old calf Kamini is gracefully bobbing up and down in the water tank alongside her mother, Kambiri. The two chase and gnaw at one another, playing up for anyone watching through the glass walls of the tank. Kamini weighs almost 40kgs but moving through the water she looks almost weightless.

“Kamini is a water baby, she loves the water,” says Tracy Roberts, senior ungulate keeper, as she gives the pair a warm shower back at their pen.

“I’ve never known infants that are as stubborn and independent as pygmy hippo calfs,” she adds. “In the afternoon the mother will come to the door wanting to come in and get fed and you have to say, ‘No, you’ve got to go and get the calf before you can come in.’ And the mother will go ‘ohhh’ and trudge back up the hill and say, ‘Calf, can you come in for me please?’, and the calf will go, ‘Oh, I don’t know mum, what about another five minutes?’ Sometimes you can hear them vocalise and you can imagine Kambiri saying ‘It is bedtime, you’re coming with me!’”

Pygmy hippos are one of the many critically endangered species kept at the zoo and, although little is known of the species, which is native to west Africa, it’s thought that as few as 2,000 now exist in the wild, with civil wars affecting their rainforest habitats and making conservation unmanageable.

Roberts has an especially strong bond with Kambiri, having worked in the exotic fauna division since her birth six years ago. “When you’ve been on that journey with an animal like Kambiri her whole life, watching her grow from a little calf into a cheeky teenager and then transform overnight into the most devoted mother, it feels wonderful,” she says.

“A lot of people go, ‘Oh you work with hippos, they’re the most dangerous animal in Africa, aren’t they?’ But pygmy hippos are a subspecies, they’re different. They’re only a fifth of the size, they have longer legs, they have slimmer muscles … They’re gentle, they’re affectionate, they’re intelligent and I think they have a sense of humour too. It just breaks your heart to think one day we could lose these animals in the wild because we don’t have the ability to protect them.

“However, we do show those big teeth a lot of respect. They self-sharpen as they come down on each other, so you have to be aware that they could accidentally injure you.”

  • Infant pygmy hippo Kamini and her mother, Kambiri, playing in the pool and being showered by keeper Tracy Roberts. Photographs by Jonny Weeks for the Guardian.

Taronga zoo has been located on the slopes of Mosman, overlooking Sydney harbour, since 1916, and the giraffes, who are fed nine times a day, have occupied the same pitch throughout that time.

The zoo’s remit has changed over the decades from purely exotic entertainment to conservation, breeding and education. Its mantra now is “for the wild” and its welfare charter states its aim is “to ensure that the life experience of a zoo animal approximates the experiences of an individual living in the wild, in quality, repertoire and in relation to its species’ natural history”.

However, the existence of captive animals still provokes much criticism. Peta, the animal rights organisation, asserts that “cages and cramped enclosures at zoos deprive animals of the opportunity to satisfy their most basic needs” and that “the zoo community regards the animals it keeps as commodities”.

Ashley Fruno, Peta Australia’s associate director of campaigns, says: “Zoos often defend their breeding programmes under the pretext of conservation but very few, if any, of the captive-bred species that do face extinction in the wild – including the elephants, rhinoceros, tigers, red pandas, gorillas and chimpanzees in Taronga’s breeding programs – will ever be released back into their natural habitats to bolster dwindling populations.”

Yet the keepers at Taronga say they do all they can to ensure the animals in their care live fulfilled, enriched lives and emphasise that they are motivated to ensure the long-term protection of each species in the wild.

  • Giraffes Nyota, Jimiyu and Zarafa during feeding time with keeper Sarah Jones. Photos by Jonny Weeks for The Guardian.

At the seal enclosure, these arguments are starkly juxtaposed. The pools cannot compare to the vast expanse of the oceans and the presence of a purpose-built “seal theatre” recalls a bygone era when animals were trained purely for human gratification. But the seals at Taronga don’t perform balancing ball acts. Rather, their performances feature behaviours designed to assist in the maintenance of their health or to highlight the perils of their plight in the wild.

When Lexie, an Australian seal lion who was rescued as an orphan pup, comes out on to the stage for a private practice session, she hops onto a wooden platform and allows the keepers to massage her abdomen with a dummy ultrasound wand – they hope she might soon be pregnant and will undergo such tests for real. And when Malie is instructed into the pool, he purposefully thrashes about with a piece of fisherman’s netting to show how easily a sea lion could become trapped by such materials in the wild.

Elly Neumann, supervisor of the seal theatre, says: “We want people to come meet our animals, come feel for our animals and understand what you can do to help them. If the public come here and see Lexie and learn about the impacts of overfishing on wild colonies then Lexie becomes an ambassador for her species out in the wild.”

  • Lexie the sea lion undergoes a mock ultrasound pregnancy test before displaying her target training skills with keeper Elly Neumann; Lexie plays with an ice block; Malie the Australian sea lion thrashing around with a fisherman’s net to show the dangers faced by sealife from unregulated fishing. Photographs by Jonny Weeks for the Guardian.

Much of the zoo’s work goes unnoticed, masked by more photogenic news such as the birth last month of a male Asian elephant calf, who looks wild-eyed and wobbly legged as he scurries around beneath his mother.

The as yet unnamed calf is the fourth to be at the zoo since 2009. Pathi Harn, the second, was thought to have died in his mother’s womb during labour but, remarkably, was born healthy and now lives at Taronga’s sister zoo, Western Plains.

Taronga also runs a wildlife hospital that frequently helps local rescued animals and such pioneering scientific projects as coral cryopreservation from the Great Barrier Reef. Furthermore, it plans to open its Institute of Science and Learning in 2018 to educate everyone from pre-school children to PhD candidates.

  • The new baby Asian elephant being showered alongside its mother and rolling in the sawdust. Photos by Jonny Weeks for the Guardian.

The Corroboree frog breeding program is another case in point. From the unglamorous surrounds of a small, modified shipping container in a staff car park, Michael McFadden, supervisor of the herpetofauna department, and his team are working to breed and safeguard a population that is on the brink of extinction. These thumb-sized amphibians, which sport vivid yellow and black patterns to signify to would-be predators that they’re toxic, are reared in strict quarantine.

“In the wild there’s less than 50 southern Corroboree frogs remaining,” McFadden says. “Both southern and northern Corroboree have been decimated by chytrid fungus, which is a disease which has been brought here to Australia in the mid-70s and spread northward. Without the zoo’s breeding program and the support of the NSW Office of Environment and Heritage, Australia’s most iconic frog would be extinct.

“A few weeks ago we did a reintroduction of 360 young frogs into disease-free enclosures in Kosciuszko national park. Some of our release sites are quite remote so, if we’re doing a reintroduction with eggs that might not tolerate a 15km hike through the mountains, we use a chopper to get in and out.

“They’re an awesome little frog to work with,” he adds. “They’re a walking frog who lives on the ground amongst the leaf litter and the stagnant bogs. They’ve only got small back legs so they can’t really jump and they don’t climb. And their stripe pattern on their back and their blotch pattern on their belly is unique like a fingerprint.”

However, the species isn’t being saved simply for sentiment. “Being extremely toxic, the Corroboree frog has no natural predators and they’re a predator of small invertebrates, so they fulfil an important role in the ecosystem,” McFadden says.

  • Michael McFadden and Lauren Hush examine Corroboree frogs, which are bred in quarantine inside a shipping container. Photographs by Jonny Weeks for the Guardian.

While some species require strict quarantine, others need tactile care. Maiya the red panda had to be briefly hand-reared by the keepers after her mother unintentionally wounded her carrying her around after her birth. In recent weeks the animals have been successfully reintroduced but, when familiar keepers enter the enclosure, Maiya soon clambers down through the tree branches to greet them – and to play with her cuddly toy.

“We have such a variety of species on the carnivore unit but Maiya has a special place in my heart because I was one of her hand-raisers,” says Tamara Gillies, senior carnivore keeper. “We like to think that the animals in our care like us and want to be around us, so it’s nice when they really do.

“Red pandas naturally carry their babies round by the scruff of the neck, which is what her mother was doing. We’re not sure why, there may have been some bacteria in Amala’s mouth, but the hard decision was made to remove her at five weeks old because she needed an anaesthetic every day. If we hadn’t have done it, she wouldn’t have survived.

“We’re doing these reintroductions each day to make sure Maiya knows she’s a red panda and so that she learns all the behaviours. But we think it’s also important to spend time with her and make sure she gets that social interaction and comfort, because we’re sort of her mum.”

Following a heavy winter downpour at the start of the day, the looming clouds over Taronga have cleared. But while the wind conditions are fine for Girri, a red-tailed cockatoo, to fly at the zoo, they’re not favourable for Khan, a peregrine falcon. Taronga’s bird auditorium is positioned at the bottom of a hill and, as bird handler Brendan Host explains, “Winds from the north and east don’t support him and can cause him to stall like a plane.”

Host has a backup plan. He and a colleague jump into a minivan and head out to a local community park while Khan, wearing a leather hood over his head, rides on his hand. Soon the bird is tearing through the sky above the park chasing bait, which Host swings on a leash. Passers by look bemused. “You’re not going to lose this one are you?” one quips.

“If an animal were to go off elsewhere, that doesn’t bother us. We’ve done enough training to get to the point that they’ll land somewhere and we can recall them,” Host says.

“Awol’s not the term I’d use for it. If it’s a bit windy, if they’re trying to figure something out, or if a wild bird comes in – something they’d not expect – that’s when they may go further afield to seek shelter. Typically they’ll land somewhere else in the zoo or in Mosman, the surrounding suburb, but they have been known to go further afield. We’ve recovered an eagle from Bondi before.”

But, he adds: “They’re the best example of providing animals liberty within our zoo: they can leave if they want to but I know, if I do my job well and cater for their needs, at the end of the day they’ll still be here.”

  • Bird handler Brendan Host with Girri, the red-tailed cockatoo, during a practice flight at the bird auditorium and Khan, the peregrine falcon, during an off-site excursion. Photographs by Jonny Weeks for the Guardian.

Host describes Khan as “majestic” and hails him as his favourite animal at the zoo – “he’s the fastest animal in the world, as if you wouldn’t pick him” – while Lemon, the sugar glider trainer, picks the echidna species – “they’re an egg-laying mammal and there’s only two of those in the world”.

But veteran keeper Paul Hare has a more ordinary choice. After 27 years at Taronga, 17 of them as a seal trainer, and despite having just inspected a funnel web spider, the planet’s most venomous arachnid, Hare says his favourite animal at Taronga is an ageing, scruffy-looking goat.

“I just have a really good rapport with her,” he says, before calling her out into the yard and letting her use his legs for an extended back-scratch. “I watched her being born, I was the first one to handle her and over the years we’ve just built up a really, really special bond. I love her.”

  • Veteran keeper Paul Hare inspecting a funnel web spider and giving his favourite animal, Eve the goat, a stroke. Photographs by Jonny Weeks for The Guardian.

For most of the keepers, the day’s work ends around 4pm when the animals in their care have been fed, mucked out, measured, weighed, monitored, trained, nursed and bred, and when the public are slowly departing the zoo bearing messages of conservation.

As Khan, the peregrine falcon, is readied for the trip back to the zoo, Host spots a flock of pelicans flying in formation overhead. “I hope they’re not ours,” he says. “Different team, if they are!”