Movie production designer Mark Friedberg had assembled ambitious scenery before, but he’d never built an ark. Then, in 2011 director Darren Aronofsky called upon him to prepare one for “Noah.”

From a special-effects point of view, it’s not like the film epic didn’t have enough challenges. Rendering every animal species on earth, for example, and creating an apocalyptic deluge. The computer-generated imagery would be copious.

For the Old Testament ark itself, though, Mr. Aronofsky and his crew decided they wanted to keep things old school. They spent nearly a year designing and building a real, physical ark as the movie’s central piece of scenery.

Building an ark of biblical proportions is easier said than done. For the upcoming film epic “Noah,” crews spent nearly a year amid actual wind and storm to build the ark at the center of the Old Testament tempest. Don Steinberg reports on Lunch Break. Photo: “Noah.”

In a clearing within a woodsy arboretum on Long Island, on dry land, Mr. Friedberg’s crew spent about six months erecting the front entrance and sides of an ark about 60 feet high, out of steel and foam designed to look like logs. For scenes in the ark’s interior, they built a three-story set to the same scale inside an armory in Brooklyn.

“We decided that it would be built to biblical proportions,” Mr. Friedberg explains. That means it isn’t a seafaring ship but a large rectangular box intended to keep Noah’s family and the menagerie afloat, specified by scripture to be 30 cubits high, 50 cubits wide and 300 cubits long (a cubit is the distance from human elbow to middle fingertip). Sunk in a cement foundation, the “ark” was framed in I-beams.

In October of 2012, Hurricane Sandy hit like some kind of cosmic message and flooded parts of New York. “The ark did fine,” says Mr. Friedberg. “It enjoyed its chance at some real weather. It did better than some of our own houses.”

There have been a few other tempests around “Noah,” which opens March 28. The director and Paramount Pictures tussled over the studio’s efforts to water down Noah’s dark side and add more overtly religious content to appeal to evangelical audiences. The budget also swelled to an estimated $125 million. One special-effects house, Look Effects, took a financial hit creating vast flocks of birds, pushing its resources to the limit. And that was just a small part of creating the visual elements of the book of Genesis with ark, animals, water and Russell Crowe.

In each case, the filmmakers combined digital and physical elements. “Films like ‘Gravity,’ for example, are really in virtual worlds,” says Matthew Libatique, the film’s director of photography. For “Noah,” he says, “The visual-effects aspects were sort of brought into our live action.”

Though the ark was built to be 165 feet long, in overhead shots it was digitally extended to look more like 500 feet. Early filming was done in Iceland, on barren volcanic landscape meant to approximate an antediluvian world that humanity had spoiled. Craggy terrain photographed in Iceland was digitally composited onto the Long Island field around the ark. Dark volcanic sand was physically placed on the set, along with tree stumps to suggest that Noah built with local lumber.

Water effects in movies have come a long way since 1956, when “The Ten Commandments” used film of water poured down a chute, played backward, to part the Red Sea.

“Digital water is improving every year—take a look at ‘Life of Pi,'” says Mr. Friedberg, who has worked with such directors as Wes Anderson and Charlie Kaufman. “But interactive water is still hard to do, so where water interacts with the scenery, and in particular with the actors, that has to be actual water.”

A section of ark was built in a small pool, for scenes where the water laps at its entry ramp. Russell Crowe was submerged into a heated water tank for some shots, though digital likenesses of people were inserted underwater as well. In one scene, Noah is standing at the top of the ark’s ramp and a wave blasts him.

“In that case we had a camera behind Noah—really a double for Noah—and hit him with a water cannon,” Mr. Libatique says.

Industrial-strength cranes were parked in front of the ark to hold overhead rain bars, like an oversize office sprinkler system, dumping gallons of water on the actors for the fateful storm. Two giant pumps and five 22,000-gallon water tanks were set up behind the ark, and 3,000 feet of pipe was laid around the set. The six custom-built rain bars were capable of pouring 5,000 gallons of fake rain a minute. The filmmakers believe that might be some kind of movie record.

Mr. Libatique didn’t care if it actually rained. “With the amount of rain we were pouring on the scene, real rain would barely compete,” he says. He was more concerned about lighting. “We had to make sure it looked like a supremely overcast, stormy day,” he says. “That was the biggest trick—how are we gonna pull this off? Are we gonna cover the sun with a giant rag in August in New York? The best way was to shoot at night and light it for day.”

So the dramatic rainstorm, including a battle scene featuring 350 extras struggling to enter the ark, was filmed at night and lit from above to look like daytime using helium-filled balloon lights.

All the rain leads to the deluge, at which point “all hell breaks loose,” says visual effects supervisor Ben Snow of Industrial Light & Magic. “A lot of that is computer graphics. It sort of starts by something that’s in the Bible but not in some older Noah movies, where the waters of the earth burst from the ground. When we were filming in Iceland, I was able to shoot some footage of some of the geothermal geysers there as a reference.”

For the disaster’s climax, stunt men were yanked by wires, then converted into digital men who, in the film, are bowled over by rushing water or sent flying into the air by CGI eruptions. Eventually water engulfs everything, with an obligatory cinematic tidal wave (not in the Bible), and the ark bobs in the digital surf.

The only real animals filmed were two doves and a raven, for close-ups, says Mr. Libatique, the cinematographer. A few animals shown sleeping are puppets. Others were made in ILM’s computers. Animals arrive in groups and settle onto three separate decks of the ark: birds up top, reptiles/amphibians/insects next, mammals below). They were digitally inserted into real footage of the ark in Long Island and into a computer-replicated version of the ark.

“It was the biggest shot we’ve ever had to render, in terms of sheer processor power, to get all those furry animals on the screen,” says Mr. Snow, referring to ILM’s work on films like “Avatar” and “Jurassic Park.” They put hundreds of processors to work. “If it was running on one processor, it would have taken about 38 years.”

Mr. Aronofsky, who directed “Black Swan” and “Requiem for a Dream,” sought to avoid standard-issue creatures. “He didn’t want them to be the sort of animals you expect in a Noah’s Ark story,” Mr. Snow says. “We did a whole lot of research even into extinct animals, like Victorian drawings where they’d only heard descriptions of animals, and they came up with these crazy versions. We also looked for real animals but unusual ones. So we couldn’t have a male lion or a zebra or a giraffe. We’d have a springbok or something less obvious.

“We did put a few pachyderms in there,” he adds. “It’s actually something the studio requested. They wanted something the audience could latch on to.”

The bird-related travails of the special effects company Look Effects involved using more than 700 computers. “Some of those bird shots have 84 different groupings of birds, all hand-animated, just insane,” says President Mark Driscoll. “We hit it out of the park, it just took a little hit to do it.”

Mr. Aronofsky and his colleagues realized that, in making a movie set before the flood, they could create their own rules about what the world may have been like back then. In the film, Noah’s world is populated by six-armed giants called Watchers, based loosely on Biblical angels, who are made out of rocks and have skin like the Thing in “The Fantastic Four.” They’re entirely computer-generated, of course. Mr. Libatique suggests that ILM’s experience making giant robots move gracefully for the “Transformers” movies came in handy.

The production designers dreamed up tools and weapons and other implements of early civilization. Noah employs a glowing energy source found in the ground called “zohar.”

They also left some things out. “No sandals, that was the first order of business,” Mr. Friedberg jokes. “This was a Bible story with no sandals.”

ModuTank supplied a modular tank for special water effects related to this production.