Kerwin Porter is a good catch. Young, lively, committed and as passionate as it is possible to be about fish. His pride isn't any old flounder, but the fish to be found in the aquarium at the Horniman Museum in south-east London. Porter is the aquarium's curator.

The Horniman's is one of a very few aquaria attached to museums in Britain. And this small shoal is swimming back into fashion. After an extensive £1.5m redevelopment, the Horniman reopened last summer to much acclaim, winning a place on this year's Gulbenkian Prize longlist. The World Museum Liverpool's aquarium, which first opened in 1857, welcomed visitors again in April 2005 after a six-year refit.

These aquaria may bring in the crowds, but is there really a place for live seahorses and jellyfish in 21st-century museums? For Porter, the answer is obvious. 'Seventy per cent of this planet is covered in water,' he says. 'You've got to include it.'

The Horniman has been home to sea anemones and starfish since it opened in 1903. Then, seawater was transported by train from Brighton on the south coast. Now the salt is artificially added to giant tanks in the basement - nearly all aquaria are below ground, for fear of flooding the museums' collections.

'The museum's philanthropic founder and avid naturalist, Frederick Horniman, wanted to show the Victorian public the living natural world close-up,' says Porter. 'We've have tried to stay true to his vision.'

Porter, who was involved throughout the aquarium's three-year development, was determined it wouldn't be just another fishy theme park. 'We're not macho and into sharks,' he says. 'We champion the little guys.'

The Horniman does have a coral reef, rainforest and mangrove swamp filled with fabulous, fluttering fish. But it also has far less exotic habitats containing more mundane specimens. 'We wanted to have a pond, but people said it was boring,' says Porter. 'People use "pondlife" as a derogatory term. We wanted to challenge that; we've done a tribute to a London pond.'

While I'm there, it's the much-maligned pond that has the most noses pressed against its glass, to witness the life cycle of the frogs or look at a lily from underneath its pad.

'In the British Isles, you're never more than 70 miles from the sea,' says Porter. 'So let's show them some beautiful British sea-life, so they don't think it's all abroad.' Another habitat is a north Devon rockpool. 'Everyone goes on about saving the rhino, but conservation begins at home.'

In Liverpool, half of the fish tanks are of native habitats. 'It's very easy to get focused on pretty places with colourful fish,' says Rachel Porter, Liverpool's senior aquarist. 'But it's important, especially with over-fishing close to home, that we see local fish.'

The aquarium at Bolton Museum has a more international approach, with fish from every continent except Antarctica. But Bolton uses its overseas aquatic collection for a very local purpose.

'The demographics of people in Bolton are constantly changing,' says Pete Liptrot, one of Bolton Museum's two aquarium services officers. 'We're always altering our displays so we can have familiarity and discussions with people who come here from displaced communities.'

No one knows why Bolton Museum has had its own aquarium since 1941. 'In fact, we were thinking of putting a competition in the local paper to try and find out,' says Liptrot. But if they didn't know why the tanks were originally installed in the museum's basement, Liptrot certainly knows why they're there now.

'People have always kept aquarium fish, and especially here in the North West. The North West is the home of aquarium keeping in the UK,' he says.

Liptrot is awash with arguments for the value of keeping giant green knifefish and red-bellied piranha in a museum, from providing 'excellent opportunities to observe a wide range of behaviours' to 'people find fish relaxing'. 'It is a place for inspiration, education and to wonder at the world,' he says.

Like many people who work in aquaria, Liptrot isn't your typical museum employee. An ex-bouncer who gave up his job when he was 'glassed' one night at work, he applied for a job at the museum aquarium 13 years ago because his mother had brought him to Bolton's aquarium when he was a child to 'keep me quiet'.

Aquaria are still great family fodder. 'When you see young children coming in, almost all will go to the aquarium first. We're very popular with families and young children,' he says.

Liptrot still puts that visitor experience at the heart of his work. 'People don't feel the need to understand fish to look at them. But with other areas of the museum - the art, for example - there's a feeling if you don't understand you shouldn't be looking at it.'

Rachel Porter at Liverpool delights in the questions visiting children ask about the fish. '"How long do they live for? Where are they from? What do they eat?" are the most popular,' she says. 'But I did get asked once if crabs believe in God. What do you say to that?'

All aquaria staff talk about the double burden of both looking after live specimens and delivering public programmes. Aquariums fall under the Zoo Licensing Act, which carries a heavy regulatory burden. 'Fish are the most ethically acceptable group to keep in captivity. You can provide a very reasonable facsimile of their natural habitat. And you have no problem with escapees,' says Liptrot.

The Horniman has not been so lucky. The pipa frogs from Guyana had to be taken from display and kept in isolation behind the scenes, as they kept jumping over the top of their tank into the one next door and eating all the fish.

Not all such jumping of barriers is bad. The aquarium staff I spoke to saw clear links between their work among the tompot blennys, and their colleagues' work among the 'dead' collections in the rest of their respective museums.

'We've got Polynesian artefacts made out of sharks' teeth, musical instruments made out of conch horns and paintings of fish,' says Kerwin Porter.

Bolton also sees itself as embedded in the wider museum. 'Wherever we can we try to create links,' says Liptrot of his work with other museum staff. 'We have a display of Egyptian fish from the River Nile. That ties in with our Egyptian collection here.'

The aquarium is involved in all new projects. 'Education staff are developing a project on food in different countries, so we're going to use the fish to get views about the way fish are seen differently by people here to, say, someone in Myanmar or Somalia,' says Liptrot. 'In these countries, fish may be purely a food source. The idea of keeping them to exhibit may be completely bizarre.'

Education is an aquarium's natural habitat. The Millennium Commission lottery project the Deep in Hull, although not attached to a museum, has a strong and increasing educational role. Over the past year, 22,000 students have made use of the Deep's learning centre, with over half from primary schools.

The in-house teachers have created a learning programme including science, English, maths, geography and art. The Deep is about to run a marine biology course in conjunction with Hull University.

At the World Museum Liverpool, the aquarium, formerly in the zoology department, is now part of learning. Visitors can examine coral under a microscope and see venomous scorpion fish being fed, swallowing their food whole.

Most school visits to Bolton Museum end with a feeding session in the aquarium. Textile and animation students are frequent visitors, drawing inspiration from the colours, shapes and movements. The Horniman trawls in students, too. 'This is a living world of art,' says Porter, with a sweep of his arm around his aquatic kingdom. 'This has inspired artists for centuries.'

Aquaria may have been pioneered in the 19th century, but they now place themselves at the helm for new ways of working with visitors.
'We see ourselves as being the way that everybody will need to go,' says Liptrot. 'Visitors rarely meet curators from other areas of the museum. Visitors always meet us. We spend half an hour talking to them about how the catfish feed. We're advocates for our discipline. We think other people in museums should do the same thing.'

Linda Conlon, the chairwoman of Ecsite-UK, the science centre network, says of aquaria in museums: 'It's innovative. The days when museums were solely collections and science centres were hands-on has gone. The distinction between these institutions is blurring. Museums are already places where people can feel and touch. Having a variety of these techniques and approaches can only encourage this experience.'

Liptrot sees his fish as the future. 'We hope, in 30 years' time, our young visitors will become icthologists, biologists, ethologists. That's what museums should be doing - inspiring young minds.' mj

Dea Birkett is a writer, broadcaster and director of Kids in Museums