Off the coast of a Caribbean island, a young couple, Lou and Lisa, flee the hotel in the middle of the night to have sex in the sea. But they swim into a sunken wreck which is also a piranha lair and they are both killed and eaten by the unseen piranha.The next day, a group of tourists, including Tyler Sherman (Steve Marachuk), are taking the diving courses provided by Anne Kimbrough (Tricia O'Neil), an employee of the Hotel Elysium. One of her divers swims into the wreck, which she has strictly forbidden to her divers. Leaving Tyler to take over and lead the others to the surface, she discovers almost immediately that her 'missing' student has swam into the wreck and been killed there when his badly chewed up body is found.Anne's estranged husband, Steve (Lance Henriksen), a police officer, refuses to listen to Anne about her wanting to have a look at the body, because she needs to know what happened. The death does not seem to match the attack pattern by any of the marine life in this area, which she knows better than anyone. For her not to know what killed a diver is a dangerous sign. Steve intercepts Gabby (Ancil Gloudon), a dynamite fisherman, and his teenage son, and threatens to confiscate their boat, but as Gabby explains, Steve, Anne, and he, are old friends.Meanwhile, as the guests begin to flirt with each other (a middle-aged widow, named Beverly, flirts with a younger man, named Leo, who is a dentist), a pair of young women, named Jai and Loretta, arrive at the resort on a large sailboat. By their own admission, they are "sea bandits". Jai sneaks into the kitchen to steal food, but is intercepted by Mal (Arnie Ross), a mentally-challenged cook. She flirts with him, and he offers instead to make her a wonderful dinner. But as he goes to their boat with the meal, they take the meal and then undock, letting the boat drift. They try to convince him to jump, and he tries, and fails, so they mock him and sail off. That night, Jai and Loretta sail too far out, and are attacked by the piranha, who have developed the power to fly. Jai is attacked and her throat ripped out while Loretta falls into the water and gets eaten alive by the fish in the water.Worried about what's going on, Anne finds that she is being frequently bothered by Tyler Sherman, and so she takes him with her to the morgue in town to get a look at the body. It is revealed there that she became a marine biologist before she married Steve, and so she begins taking pictures. There, she finds that the body of the tourist has been eaten in many parts. A nurse comes in, kicks them out, and ends up quickly dead, for a piranha was hiding in the body and escaped in it. Armed with the power to fly, it kills the nurse by biting her throat out and escapes out a window into the night.In her hurry, Anne left her credit card behind at the scene. Anne and Tyler have a one night stand back in her room. But the next morning, while he sleeps, she begins to study the pictures, and is horrified by what she discovers. Steve arrives, throwing the credit card at her, angry first that she went to the morgue in defiance of him, and secondly that she has man in her bed. She tries to warn him of what she's discovered, but he ignores her and thinks she's a murderess.Anne tries to tell Raoul (Ted Richert) the pompous hotel manager, that she's canceling the dives because it isn't safe. Raoul at first pretends to be concerned, but swiftly fires her, thinking she is crazy. Attempting to capture one for further study, or at the very least take some pictures so she can prove what she's trying to tell Steve and the manager, she is intercepted by Tyler, who swiftly informs her that he is a biochemist and member of a team which has developed the ultimate weapon: a specimen of genetically modified piranha, with some other fish's genes intermixed, capable of flying. Earlier, and unfortunately, the team mistakenly deposited (or lost) a cylinder full of these fish when a cargo ship was sunk the water where the dead couple were found.Aaron provides the proof Anne needs to Steve, calling him and showing him, not merely some flying piranha he's recently caught, and never seen before, but also that they're a serious danger, because they're turning on each other. This is a sign that they're running out of food and will soon attack whatever they come near, including humans.At a meeting, Anne tries her best to reason with Raoul, to no avail. Steve surprises her, standing up for her and proving her case for her by throwing the body of a dead piranha onto the table. Steve tells her that she can't trust Tyler, because the army says he's crazy. She argued that Tyler's just been using her to get the message of the piranha out for him, to protect both himself and the residents of the hotel.Later that evening, a piranha attacks Gabby's son and kills him in his shack, leaving a bereft Gabby to vow revenge by killing the fish in the wreck they hide in. Anne tries to dissuade him, but it's too late. Having ignored Anne's advice, Raoul hosts a nighttime fish party to capture grunion, who come up to the beach to spawn at this time, making them easy prey for humans to capture and kill. Unfortunately for the residents, the piranha are also partially grunion and share the same instinct. During the fishing party promoted by the resort, the piranhas fly out of the water and attack the guests on the beach and at the hotel's courtyard pool. Anne leads those who survive into hotel, where they shut the doors and windows. Gabby tries to attack them, but they overwhelm and kill him as well.In the morning, the piranha withdraw, for Anne had discovered that they are not fond of daylight. Tyler and Anne decide to undertake Gabby's plan, and blow up the ship to destroy the predators. Meanwhile, the situation gets even tenser, for not merely can the piranha fly, but Anne and Steve's teenage son Chris (Ricky G. Paull) has been hired, against their wishes, by a local ship 'Captain', and his lovely daughter Allison (Leslie Graves). Chris and Allison sail away, and strand themselves on an island, leaving them vulnerable to piranha attacks that never actually happen. Getting lost at sea, they try to set sail again, heading straight toward the wreck.When Chris and Allison are stranded in a raft above the shipwreck, Annie and Tyler arrive in a motorboat and don scuba gear to dive down to the wreck to plant the timer charges that Aaron left behind. With only 10 minutes to get out of the wreck before the bomb explodes, Anne and Tyler are trapped in one of the sunken ships rooms by the murderous piranha who all return to the wreck. On the surface, Steve, piloting a police helicopter, ditches the chopper and swims to Anne and Tyler's motorboat where Chris and Allison are. With minutes left to spare before the bomb explodes, Steve powers up the boat and takes off. Down in the wreck, Tyler sacrifices himself to allow Anne to escape out of a porthole and to tie a survival rope around her waste allowing herself to be pulled away by the motorboat on the surface. At the last second, Anne gets clear and the bomb detonates, destroying the sunken ship and the piranha with it. With all the murderous fish dead, Anne swims to the surface and is picked up by Steve and the two kids in their boat.