After filming in Spain for three weeks, the filmmakers traveled to England for ten weeks of filming on sets constructed on the enormous stages at Elstree Studios. Interiors created by production designer Elliot Scott included Walter Donovan's apartment overlooking Central Park, sinister Venetian catacombs, and the interior of a zeppelin.

To facilitate the action onboard a steamship off the Portuguese coast in a raging storm, a forty-foot-by-sixty-foot section of deck was constructed on large gimbals to produce the requisite rocking motion. "We also had wind machines blowing and a dozen dump tanks filled with water," said George Gibbs. "On this small piece of set, the actors and stunt people were trying to act while tons of water fell on them. It was a pretty shattering experience. One of our dump tanks held three hundred gallons - three thousand pounds of water-and when we let two of them go at once, it would knock people clear across the deck."

"The sequence on the boat seemed to be the toughest for everybody," George Lucas observed. "It was the scariest and the hardest to do. Everyone was thrown back and forth on the deck. Scenes like this are actually more difficult to do than dangerous stunts, because on the stunts you take so many precautions to make certain no one gets killed. But storm scenes like those on the boat you cannot really control. Everyone was getting battered around."

"Nobody likes to be wet," Spielberg elaborated. "Plus, it was cold. We shot the sequence in what you could call wintertime -it was the coldest summer in London's history-and we did not have any water warmers, so the water was ice cold. Anyone who was not up before the first shot was definitely wide-awake afterwards. When we came to work in the morning, all of us got into out raincoats - except Harrison who couldn't wear anything but his fighting clothes. I just think it irritated everyone. Nobody wanted to be underwater for three days-and after Jaws, I hate water anyway."

The interior of the Grail Temple was filmed on an elaborate 80 feet into the air set designed once again by Elliot Scott. Suddenly the whole temple begins to shake, the floor heaves up and splits and the Grail slips out of Elsa's hands and into the fissure. "The temple sequence was one of the reasons I told George Lucas that this movie was the hardest I had ever worked on," George Gibbs commented. "The set was about the same size as the one in The Temple of Doom and we only had about six weeks to build it. We had five main gimbals to make the floor split open and heave up. Then we had more gimbals to make columns fall down and open trapdoors - a total of about ten gimbals in all. Fortunately, resetting took only about twenty minutes. Since everything was hydraulic, we simply put the set back to the start position and filled up the cracks with plaster." One effect the filmmakers were unable to do on the full-scale set was the moment when the Grail falls out of Elsa's hands, strikes the temple floor and causes the stone surface to crack open. "The shot was attempted on location," noted visual effects supervisor Michael McAlister, "but it was a very difficult thing to accomplish. We did it about a thousand times ourselves. It was one of those shots where you say, 'Oh, yeah, cracking floor - that's easy,' and then it takes two months, off and on, to get it right. We actually built a full-size floor section about twenty feet square, prescored a crack and sealed it up with plaster and sand. Then we tossed an epoxy version of the Grail in from about six feet away. That turned out to be the most difficult part of the shot getting the Grail to land in precisely the right spot. Once we did, we pulled levers hooked to each side of the floor to literally separate the two halves of the set and form the crack."

Continuing the grand horror tradition from the previous two films the script featured a scene of Indy exploring catacombs beneath the streets of Venice that contained mummified bodies, channels filled with petroleum water and thousands upon thousands of rats, the grossest of all vermin (a scene inspired by From Russia With Love). The production team made an order of 1000 sewer rats to Animal Actors in December 1988. The animal expert who had supplied the previous two Indiana Jones films with vast numbers of snakes and insects suggested that they should breed their own army of rodent extras. "Gray rats are hard to find," noted Robert Watts, "but they breed fast and we had plenty of lead time. It took us only about four or five months to get all the rats we needed." At the end they came up with 6000 rats. For the safety of cast and crew each of the rats had been certified free of disease. When the time came to film the scene every inch of the wonderful set created by Elliot Scott was covered with them. No stone was left uncovered. And as had happened on the proceeding two movies at least half of the crew hated rats and had to wait outside the stage until filming was completed. "Same thing happened with the snakes. We lost half the crew on the first movie, and we lost three-quarters of the crew with the bugs," recalled Spielberg. Although in start it was not an easy alliance soon cast and crew came to like to their fury co-stars. "That kind of stuff doesn't bother me at all," said Ford, who was seen playing with a rat during a break. "The rats didn't bother, the snakes didn't bother me. It's the people I'm scared of." Doody, too, appeared braver than Karen Allen and Kate Capshaw did opposite their animal co-stars, "Most of the creatures, and bugs, or whatever, that I was involved with I thought were more frightened of me than I was of them."

Animal expert Mike Culling worked with wranglers and animal trainers to provide the right horses, lions, rats, and snakes for filming. "Harrison Ford is very good with animals and carefully prepares for working with them and handling them," animal consultant Mike Culling said.

"I found the rats easier to work with than the snakes and the bugs in the previous films," observed Frank Marshall, who doubled as second unit director for many of the action scenes. "Like the bugs, however, they had a tendency to go where we didn't want them to. Snakes move so slowly that it's easy to plunk them down in a place and then get a good shot. But rats and bugs swim fast and they move fast, and once you put them down on a set they immediately go away from the light. Still, I think we got some great shots." Concerned about the safety of several thousand four legged extras, the filmmakers opted to mass-produce a thousand artificial rodents, including a multitude of vermin mechanically articulated to swim, most of which were come to fiery end as the catacomb erupts into a subterranean inferno.

The atmosphere on the set was constantly light thanks to the production's two stars. One of the most serious scenes in the film was the one inside the zeppelin where Indy and his father discuss for the past trying to short things out. The temperature was in the hundreds and very uncomfortable, particularly for Connery, wearing a three-piece tweed suit, and Ford, sporting his standard leather jacket. Because the actors were only being shot from waist up Connery dropped his trousers. At first, Ford didn't like this but soon his face dripping with perspiration, he followed suit. They both sat there for the remainder of the serious father and son dialogue minus their trousers.