While being fitted for her pregnancy prosthetic - which involved being wrapped in a full body cast - Cate Blanchett fainted. The actress was rather surprised by this as she had never fainted before and learned in the next few days that she actually was pregnant.
Cate Blanchett never rehearsed with the crew and hadn't even met most of them before filming the nighttime electric jellyfish scene in which she first appears in the movie to add spontaneity to the scene.
The film is dedicated to Jacques-Yves Cousteau; Cousteau's ship was the Calypso. Zissou's ship is called the Belafonte; Harry Belafonte became famous singing commercialized calypso songs. In the beginning sequence, when Zissou is first introduced to the Italian audience, the model of the Belafonte on his desk is actually a model of the Calypso, painted blue instead of black.
Matthew Gray Gubler (Intern #1) sprained his ankle while filming a scene where the interns are exercising (the take where he falls made it into the final cut of the film). Gubler always wears mismatched socks and attributes his bad luck to having worn matching socks that particular day for the first time in several years.
Writers Noah Baumbach and Wes Anderson named several of the places and crew members in the film spontaneously after things and people they saw around them at the Italian restaurant where they held many of their meetings about the film. Pescespada Island, for instance, was named for one of the dishes on the menu. Some of the characters' names are named after waiters and patrons at the restaurant.
Wes Anderson watched many films set on the ocean to see how the sea movement was simulated. He found that in The Black Stallion (1979) there was only one scene set in a hallway that had the camera rocking, and so he decided to have just one rocking hallway scene in "The Life Aquatic".
Bill Murray would serenade the cast and crew in moments of downtime to stave off boredom. Murray, however, is not noted for his musical abilities so Owen Wilson bought a fusball table to keep everyone entertained.
As a pilot, early in the film, Ned Plimpton wears a Rolex GMT Master. This watch is popular with airline pilots for calculating time zones. By the end of the film, he has given up the GMT and plumped for a Rolex Submariner, for obvious reasons.
Gwyneth Paltrow was originally set to play Jane Winslett-Richardson, but couldn't because of schedule conflicts. Nicole Kidman expressed interest and Wes Anderson hired her. Kidman was forced to bow out due to other commitments, and Julianne Moore requested the role. However, it eventually went to Cate Blanchett. Anderson admitted the character name was inspired by actress Kate Winslet. Blanchett played the part while actually pregnant.
The shot of Steve Zissou feeding a fish to a killer whale, which appears during a montage on Zissou's island, was also in the script for Wes Anderson's earlier film Rushmore (1998) (where it was written into a montage when Bill Murray's character is looking at fish specimens for his new aquarium)
In Wes Anderson's earlier film, Rushmore (1998), there is a shot of Max Fisher on his go-kart which is a direct homage to a Jacques Henri Lartigue photograph. The man in this photo, as well as others taken by Lartigue is named Zissou.
There is a direct Star Wars reference at around 01:06:30 as the Belafonte comes into Port Au Patois. The seaman on the crows nest is looking through a white pair of binoculars which look very similar to the macrobinoculars that Luke Skywalker uses on Hoth in Star Wars: Episode V - The Empire Strikes Back (1980). The following cut shows the view of Willem Dafoe through these binoculars as he is yelling "Port Au Patois" to the crew. This shot, seen from the POV of these binoculars, is almost identical to the look of Luke's macrobinoculars in Star Wars: Episode IV - A New Hope (1977) as he views the Tusken Raiders from the cliff top. So really, two Star Wars references.
During filming the Chicago Cubs made a deep run into the Major League playoffs, mounting a 3-1 lead in the NLCS. Bill Murray, a native of the Chicago area, had it written in to his contract that he receive a live feed of all the Cubs' games. The Cubs eventually lost the series to the Florida Marlins, prolonging its World Series drought to 95 years.
Matthew Gray Gubler really twisted his ankle, and it made it into the final cut. He states that it is one of the things he either laughs about, or despairs, depending on his mood. He blames it on the fact he wore matching socks, as he superstitiously believes odd socks are good luck, after his grandmother told him matching ones were bad luck. Every day before and after he wore odd socks, and that was the only time something like that went wrong, when he wore matching ones.
The trivia items below may give away important plot points.
Seymour Cassel has a brief role as Esteban, the friend of Steve Zissou who is eaten by the Jaguar shark. According to Roger Ebert, Cassel once told him in an interview many years previously that he had always wanted to be eaten by a shark in a movie.
When Steve discovers the pirates playing cards, Hennessey wears a t-shirt with "I'm a pepper" written on it. This is the same T-shirt worn by the gun seller in Wes Anderson's original Bottle Rocket (1994) short.
When Steve Zissou stumbles on the kidnappers playing cards, one of the kidnappers can be seen wearing a hat featuring the Longhorn logo of the University of Texas. Wes Anderson graduated from the University of Texas at Austin.