Billy and Sheena Deep are spending their summer vacation on the Caribbean island of Ilandra with their uncle named Dr. Deep; who goes simply by Dr. D. Dr. D's assistant, a muscular graduate student named Alexander DuBrow, serves up lunch to the children: chicken salad sandwiches.
Only his cooking's terrible, so Dr. D offers to grill some fish for dinner. Billy overhears a private conversation between Dr. D and representatives for the Marina Zoo. The zoo crew wants Dr. D to find and trap a mermaid that has been reported in the area. The zoo offers Dr. D the princely sum of one million dollars.
Billy is too excited to sleep, so he goes out early the next morning at 6:30 AM to search for the mermaid. Billy's night swimming is suddenly interrupted by a hammerhead shark that almost kills him. Fortunately, the mermaid comes and attacks the shark, saving Billy's life. Dr. D nets up both Billy and the mermaid and drags them onto the deck of the ship. Billy tries to argue that the mermaid saved his life. But the mermaid is put into a large glass tank on the deck until the zoo crew arrives. Billy is enjoying dreams of Sea People, when his slumber is interrupted by the sound of crashes and a splash. Above deck he discovers the mermaid is in the process of being kidnapped! The men brutally toss Billy into the tank. Billy starts yelling for Alexander, as Dr. D is knocked out on the floor and Sheena is offering no help against the four burly men. Finally Alexander does show up, only to side with the thugs.
The thugs toss Sheena and Dr. D into the tank, lock it, and then throw it into the water. The top of the tank is meshed, so the three characters inside the tank fight to break the locks before the tank submerges completely underwater. As they struggle, the "kidnappers" and Alexander speed off, mermaid in tow. Just when things look their worst, a myriad of mermaids appear and hoist the tank above the water level. Dr. D and the children break open the latches and escape to the dinghy. As the other mermaids rescue her, the thugs attempt to set fire to Dr. D's dinghy. The mermaid is set free. Billy sneaks out by the coral again in hopes of catching the mermaid to say goodbye.
When Billy is searching for the mermaid, he is attacked by a sea monster which he encountered in the beginning of the novel.
After Scholastic made Creep from the Deep, they made a remake of the Deep Trouble novel. It released on March 2008. The book has special features in the back, and also has a raised cover. Though, the remake's cover looks almost identical to the original one.
- This book was never adapted for an episode of the Goosebumps television series, though its sequel was. However, when adapted for television, the sequel was retitled simply "Deep Trouble", which can lead to confusion to the viewer who could would expect it to be adapted from the original book instead of its sequel.
- Billy and Sheena's father was inadvertently named in the book. Billy is William Deep Jr., so that makes the father William Deep Sr.
- This story was adapted as a comic book in the Goosebumps Graphix book, Terror Trips drawn by Amy Kim Ganter.