In the tranquil coastal town of Cypress Beach, California, a meticulously organized police investigator named Scott Turner prepares for his transition to the Sacramento Police Department. He is training his successor, David Sutton, hoping for a more exhilarating career ahead. During a visit to the pier, Turner introduces Sutton to the local seafood plant owner, Walter Boyett, while also catching up with his friend Amos Reed, a shipyard junk collector. Though apprehensive about visiting Amos's houseboat, Turner is soon confronted by Amos's fierce Dogue de Bordeaux, Hooch, who seems to take an instant liking to him. However, Amos warns Turner of dubious activities happening at Boyett's plant.
As the two police officers leave, they respond to a call from Pinecone Beach, where siblings Mike and Christine Harper stumble upon a plastic bag containing over $8,000. Turner informs their mother, Mrs. Kathy Harper, that if the money remains unclaimed, the children can keep it but must allocate it for their education.
Later, that night, Boyett instructs his henchman, Zack Gregory, to eliminate a worker named Ferraday who has stolen cash. Hearing Hooch's loud barks, Gregory proceeds to Amos's houseboat, and after Amos rebuffs his bribe, he is stabbed to death right in front of Hooch, who escapes and pursues Gregory.
The following morning, Turner arrives at the scene of the murder and, although shaken by the loss of Amos, he fights to stay on the case despite federal agents Harley McCabe and Jeff Foster trying to wrest control. He successfully persuades his boss, Chief Howard Hyde, to allow him an extra week to track down Amos's killer.
When animal control officers announce that Hooch might be rabid and threaten to kill the dog, Turner defends Hooch, stating that he is a crucial witness, and takes him to the town's veterinarian, Emily Carson. After discussing the murder, Emily encourages Turner to take Hooch home, believing the dog will help him solve the case.
While reviewing the autopsy report, Turner deduces that Amos's murderer is likely military trained, inciting frustration from Chief Hyde over the investigation's expenses. In a comical turn of events, Hooch wrecks Turner's house while he shops for dog food. This leads to an awkward yet romantic interaction between Turner and Emily when he unwittingly returns to her veterinary clinic.
A breakthrough happens when Hooch spots Gregory at a wedding across the street, prompting a chase that reveals Gregory as a prime suspect. After learning that he is a former Marine connected to Boyett, Turner seeks permission for a search warrant, but when nothing turns up, Chief Hyde passes the case onto Sutton.
Despite maintaining a romantic relationship with Emily, Turner decides to keep a watchful eye on the plant. During a covert stakeout, he discovers a connection between the stolen cash and a box of similar bags, leading him closer to the truth.
In a tense confrontation, Turner tracks Gregory to a motel, but is held at gunpoint. However, with Hooch’s intervention, Turner manages to subdue Gregory, who then confesses to killing Amos and exposes Boyett's illegal operations.
Upon returning to the plant, now equipped with the truth, Turner prepares to uncover the hidden secrets behind Boyett’s empire, leading to a climactic showdown that reveals not just corrupted loyalties but the strength of teamwork with Hooch. Amidst a thrilling gunfight, which results in tragedy for Hooch, Turner ultimately confronts the chief and uncovers the extent of the conspiracy, culminating in a bittersweet ending where Turner inherits not just the role of police chief but also a legacy from his beloved canine partner.
In the aftermath, Turner marries Emily and cherishes the new puppies stemming from Hooch, ensuring that his loyal friend will always live on in spirit.
