To the amazement of archaeologists, the area was found to contain hundreds of 3,000-year-old wooden posts, which once held up a long palisade and a timber platform about the size of Wembley Stadium.
These posts crossed the marshy fenland during the Bronze Age, and were saved by the watery peat that has entombed them. The platform has now been flooded to protect it, but some of the posts are still being studied, and are on show.
It is also fascinating to see a section of the road the Romans built on top of the Bronze Age route.
To help visitors step back in time, archaeologists have reconstructed a Bronze Age landscape, including huts, and breeds of domesticated animal that would have been in use at the time, but are now rare.
Some of the thousands of finds - including weapons, jewellery and sacrificial items - are on display in Flag Fen's small museum, housed in the visitor centre. The museum itself is unusual. Foundations below 18in are banned at such an important site for fear of damaging whatever still lies buried. So the visitor centre is floating over the re-created mere.
Lucy Winson, from St Ives, Cambridgeshire, took her son Oliver and his friend Matthew, both aged 11.
Lucy: It was nice to see the enthusiasm of the guide who took us round. She captured our attention and made it much more interesting. I live about 35 miles away from Flag Fen, and I'd never heard of it - and I'd had no idea of its importance or significance to archaeologists. It's a good afternoon out.
The facilities were good - and there were some added touches, such as the umbrellas we could borrow if it was raining. I was pleasantly surprised by the information on display.
The animals were a good addition - giving you an idea of the sort of stock that was kept on this site thousands of years ago - and they also add a bit of interest for younger children. But I don't think my two younger ones would have appreciated Flag Fen. It's more suitable for children of secondary school age.
Oliver: When we first came in it looked as if it was going to be a small place. I didn't think it would be a gigantic park, like a village. I liked the animals, especially Angus the goat. I know people used to live in huts, but I didn't expect it to be like it was. I thought it was just the Saxons who had huts like that.
During the visit I learnt how people lived in the Bronze Age, how they built their houses, what sort of things they did in a day, and how they sacrificed animals. I also liked seeing the excavations.
But I have to say, this was not one of the most interesting things I have ever done. It was OK. This would be a good place to come for a school trip if you were doing the Romans, because we saw a Roman road. There's a great souvenir shop, and we bought some Roman figures and two cannons.
Matthew: I am not sure that I would like to live in the Bronze Age environment because they had no air-conditioning, no lights, no electricity; it was draughty and they didn't have comfortable beds, by the looks of things. I prefer my home. I have learnt from this that history can be very different from the way we live now, and that the past could be vicious. It was much more dangerous - especially living in a watery environment.
Flag Fen is at Fourthe Drove, Fenage, Peterborough (01733 313414). Open daily, except 25 and 26 December, 10am-5pm (latest admission 4pm). Admission: adults pounds 3.50, children/ students pounds 2.50, under-fives free, family ticket (two adults and three children) pounds 9.50, discount for English Heritage members.
Shop: sells souvenirs, postcards and a good stock of books.
Education: special tours and visits for schools feature hands-on experience, and videos that fit in with the National Curriculum.