The festival's second stage, where bands such as Kula Shaker and the Chemical Brothers are supposed to be playing, was closed down after fears that it was sinking into the mire.
But the weather has its positive side. "I think it has stopped the hedge- jumpers this year," said Michael Eavis, who owns the farm where the festival is being held. "Ticket-holders are coming, but the eco-warrior problem has been solved."
At the last festival two years ago an estimated 20,000 people got in free after environmental activists pulled down a section of the 20ft fence that surrounds the site.
The police, too, were happy with the weather. "We reckon that the rain is worth an awful lot of policemen," said Inspector Keith Jones, of the Avon and Somerset constabulary. "It tends to relax things down. People are too tired from walking in the mud to get up to anything."
The police had received 169 reported crimes by mid-afternoon yesterday, about 100 less than at the same time at the last festival. There had been 49 arrests for drugs, including one unhappy camper who tried to bring in a cannabis plant.
Despite warnings that the 300 police on the site will arrest those they see using drugs, many of the festival's devotees believe it is still a major reason for coming. "I like coming, because I can smoke hash in public," said Phil Simmons, 30, from Scotland. "It is as if we have legalised it for a weekend."
Few people were willing to let the mud get them down. "You could tell it would be chaos before you got here," said Mark Nash, 32, of Exeter, Devon. "So you just made sure you had your wellies and a waterproof. After all, mud is just mother-earth," he said sarcastically.
He added: "The rain makes it interesting. People at first were pissed off, but eventually they get used to it and there is more a feeling of community than on sunny years. It is us against the elements."
"There's no pressure here," said Mel, 28, from London. "You wander about, watch a band, have a beer, have a spliff, do what you like. I enjoy it more when I don't bother trying to see a particular band and the mud becomes comical eventually."
Others were less laid back. Security guards had to be called to manage a mob at a market stall selling Wellington boots. "We sold 500 pairs in 40 minutes," said Alan Jackson, of the traders Joe Bananas. "No one got hurt, but wet, wellie-less people can be scary."
Another 6,000 pairs of Wellingtons were being brought in late yesterday to meet the demand. At the medical centre a steady stream of sprained ankles and cuts were being treated by a harassed team of doctors. Most people had fallen in the mud, but only 12 had needed medical attention overnight, mostly for exposure.
In Glastonbury's welfare centre, in a disused barn, ad hock clothes lines were strung from the rafters covered in muddy clothes while their dishevelled owners huddled in blankets near gas heaters.
"The things that are normally difficult here become a lot worse," said Mary Treacy, who runs the medical centre.
"Things like a bad trip, or getting lost are a lot worse when you've fallen over in the mud. Mind you, it gives a lot of them something to moan about," she added.
Mr Eavis maintained that he was still enjoying himself despite the mud. "But I don't think I'd be so keen if it was like this every year."