Claire Spencer (Michelle Pfeiffer) lives in Vermont with her husband Dr. Norman Spencer (Harrison Ford), an accomplished scientist. After dropping her daughter Caitlin (Katharine Towne) off at college, Claire begins to notice the activities of the couple who have moved into the house next door, the Feurs.
Overhearing Mary Feur (Miranda Otto) sobbing one day, Claire becomes concerned when Mary tells her she is afraid she may disappear. When she sees Mary's husband Warren (James Remar), a colleague of Norman's at the college, dragging a suspicious form in the middle of the night and putting it in the trunk of his car, she suspects he has killed Mary. Claire decides to investigate. After nobody answers the door, Claire soon witnesses strange occurrences when she is alone in the house and becomes convinced that Mary is dead and haunting her. Desperate to reach Mary's spirit, Claire invites her friend Jody (Diana Scarwid) to join her for a séance in her bathroom. The séance provides no results except for the dog scaring them, so Jody leaves after Claire confides that Norman treats her like a child due to her car accident a year before and the recent departure of their daughter. Claire then cleans out the bathroom, but then returns to it with a full bath tub and a steamy message on the bathroom's mirror that reads "You know". Hysterical, Claire runs downstairs to get the phone when the computer (that turned on by itself after she went upstairs earlier) begins to type "MEF" over and over. Terrified, she then runs to her husband's office at the college where he accuses her of attempting to sabotage his career. She denies it, but then realizes that Warren is there and she confronts him only to find that Mary is with him and alive. Mary visits her the next day and apologizes for the misunderstanding, explaining that she briefly left her husband because of their volatile fights with each other. Claire returns to the therapist she recently began seeing.
Despite the resolution with the Feurs, Claire continues to experience strange phenomena in her house. She sees the ghostly image of a woman in the lake from her dock, and finds a silver key beneath the screen of a floor vent. After a picture falls and breaks, Claire notices a newspaper clipping about a missing girl named Madison Elizabeth (Amber Valletta). She then does some more research which informs her that Madison's last name is Frank (fitting the initials MEF) and she resembles her, but with green eyes as she had mentioned to Jody. She also learns that Madison attended the university where Norman works, and that the police assumed she simply ran away a year ago. Claire then visits Madison's mother and is taken to her room, where she sees her full picture. Later, Norman comes home and Claire seduces him, but right before consummating things her face turns into Madison's and Norman pushes her away roughly. Claire comes to her senses and the memory of her own car accident returns as she remembers that she had caught Norman and Madison together. Distraught by the discovery, she had crashed her car into a tree while driving in a rain storm. They argue and Claire leaves.
Outraged by Norman's infidelity and the nasty things he said during their argument, Claire spends the night with Jody. While talking, Jody confirms that she had her suspicions of Norman's infidelity when she spotted him with a young woman in the nearby town of Adamant. The next morning Claire returns home and finds Norman comatose in the tub with a hair dryer. The paramedics are called, but he is given a clean bill of health and warned to get checked out soon. Claire is convinced that it was an attempt by Madison to take revenge, and that her spirit has now been appeased. Norman confesses to Claire that while he did have an affair with the girl, he played no part in her disappearance.
Seemingly reconciled with Norman, Claire visits Adamant, where she spots the same key-necklace in a shop window along with a chest it unlocks. That night, she dives into the lake and uncovers the box, unlocking it with the key and finding the matching necklace. Norman interrupts her and alters his story: after breaking off his affair with Madison she was so distraught that she committed suicide by overdosing on pills in the Spencer house. In a panic, he placed Madison's body into her car, which he then pushed into the lake, and threw the chest with his matching necklace in it into the lake as well.
Claire is unmoved by Norman's explanation and tells him the only way to make it right is to notify the police and bring Madison's body up from the lake. Norman pretends to speak with the police on the phone and agrees for an officer to come to the house. When he leaves to take a shower, Claire redials the phone and discovers that he called 411 (information), not 911. Norman grabs her from behind and sedates her with a paralyzing drug. He drags her to the bathtub and leaves her to drown in the rising water, so that she will appear to have committed suicide. In the midst of this Norman then confesses to Claire that his previous story had been a lie: he killed Madison to prevent her from going to the Dean about the affair and ruining his career. He intimates that he hopes Claire's death will bring him closer to her daughter Caitlin. As he leans in for a final kiss, he spots Madison's necklace around Claire's neck and tries to remove it. Claire's face takes on the image of Madison, and in shock Norman slips on the floor and bangs his head on the rim of the tub, knocking him out.
Claire, recovering from the paralysis, barely manages to shut the tap off in time to save herself from drowning. When she regains her strength, she finds that Norman is missing from the bathroom floor. She crawls down the stairs to the phone, and notices Norman apparently unconscious, his head bleeding profusely. As she reaches over him and attempts to make a phone call, he grabs her ankle and in a blind panic she rushes out of the house, grabbing the car keys and a cellular phone and driving away in a truck with the couple's sailboat hitched to the back. As she is crossing the bridge over Lake Champlain, Norman bursts through the back window and grabs Claire; she frantically dials 911 and the truck careens down the embankment into the lake.
Underwater, Claire escapes out the window, but Norman grabs her leg. Madison's body floats up and grabs Norman; literally scaring him to death. This forces him to release Claire and Madison takes Norman back below with her. The truck dislodges Madison's sports car, revealing where she has been.
That winter, Claire places a single red rose on Madison's grave.Harrison Ford as Dr. Norman Spencer
Michelle Pfeiffer as Claire Spencer
Diana Scarwid as Jody
Miranda Otto as Mary Feur
James Remar as Warren Feur
Katharine Towne as Caitlin Spencer
Ray Baker as Dr. Stan Powell
Joe Morton as Dr. Drayton
Amber Valletta as Madison Elizabeth Frank
Wendy Crewson as Elena
Documentary filmmaker Sarah Kernochan had adapted a personal experience with the paranormal as a script treatment featuring a retirement aged couple dealing with restless but compassionate spirits. DreamWorks commissioned a rewrite from actor-writer Clark Gregg. This script was later delivered in 1998 by Steven Spielberg himself to his director friend Robert Zemeckis, who had signed a deal for DreamWorks to distribute the films of newly founded production company ImageMovers, and announced interest in doing a thriller film. Harrison Ford then signed to star on the film, even agreeing to clear room in his schedule for the project. Michelle Pfeiffer then followed as DreamWorks started to deal with 20th Century Fox regarding the film's distribution. Ford and Pfeiffer were Zemeckis' first and only choices for the lead roles. Fox agreed to distribute both What Lies Beneath and Zemeckis' other project Cast Away, with the thriller having Fox doing the domestic distribution and DreamWorks the international one.
Zemeckis filmed What Lies Beneath while Cast Away was shut down to allow Tom Hanks to lose weight and grow a beard for his character's development. As Gregg had to remain with production for rewrites, he had to decline Aaron Sorkin's offer to read for a major role in Sports Night - though Sorkin would later write for Gregg a minor role in the final episodes of the series.
What Lies Beneath opened in 2,813 theaters in North America and grossed $29,702,959 for an average of $10,559 per theater. The film ended up earning $155,464,351 domestically and $135,956,000 internationally for a total of $291,420,351 worldwide, close to triple its production budget of $100 million
The film received mainly mixed reviews. The film currently holds a rating of 46% on Rotten Tomatoes based on 124 reviews with an average rating of 5.5 out of 10 with the site's consensus stating that "Robert Zemeckis is unable to salvage an uncompelling and unoriginal film." The film received a score of 51 on Metacritic based on 35 reviews.
The New York Times wrote that, "at the start, [Zemeckis] zaps us with quick, glib scares, just to show he still knows how, but his heart isn't in this kind of material anymore. His reflexes are a little slow." The Los Angeles Times called it "spooky with a polished kind of creepiness added in... What Lies Beneath nevertheless feels more planned than passionate, scary at points but unconvincing overall." The Chicago Sun-Times wrote: "Lacking a smarter screenplay, it milks the genuine skills of its actors and director for more than it deserves, and then runs off the rails in an ending more laughable than scary. Along the way, yes, there are some good moments." Time Out thought that, "after a slow build that at times makes every hair stand on end – Zemeckis rolls out every thriller cliché there is. A pity, because until then it's a smart, realistically staged, adult-oriented and extraordinarily effective domestic chiller." Empire wrote: "The biggest surprise is, perhaps, that what emerges is no masterpiece, but a semi-sophisticated shocker, playfully homaging Hitchcock like a mechanical masterclass in doing ‘genre’. The first hour is great fun... It’s an enjoyably giddy ride, certainly, but once you’re back from the edge of your seat, you realise most of the creaks and groans are from the decomposing script."
Michelle Pfeiffer received some positive notice for her performance. Roger Ebert called her "convincing and sympathetic."
In his review, Ebert said that he felt the problem with Zemeckis' desire to direct a Hitchcockian film was to involve the supernatural (the film contains several musical, visual and plot references to Psycho and Vertigo, among other Hitchcock films), which he believes to be something Alfred Hitchcock himself would never have done.
Harrison Ford and Michelle Pfeiffer both won Blockbuster Entertainment Awards for Favorite Actor – Suspense and Favorite Actress – Suspense, while Diana Scarwid was nominated for Favorite Supporting Actress – Suspense.
The film received three Saturn Award nominations, for Best Horror Film, Best Director (Robert Zemeckis) and Best Actress (Michelle Pfeiffer), but lost to Final Destination, Bryan Singer for X-Men and Tea Leoni for The Family Man, respectively.