After their dad has a debilitating stroke, Price, Ephriam and Brynn Appledore-Smith move to the family’s ancestral home in Maine with their mom and dad. Located in the town of Crystal Springs, population 1,716, the house is a castle with winding passageways.
Generations earlier, Angus Appledore moved his family from Scotland as part of his ongoing quest for the fountain of youth. By the early 1900s, the Appledores had made a fortune from bottling the area’s water and opening a resort, which touted the water’s healing properties. This is why the house is known as the Water Castle. Orlando Appledore, Angus’ great-great nephew, carried on the research, hoping to prove scientifically that there was something miraculous in the water.
The kids pick rooms for themselves in the meandering house. Eighth-grader Price wants the strange room on the third-and-a-half floor. Ephriam, a sixth-grader, picks a room with a bathroom attached so he can finally have some privacy. Seven-year-old Brynn, a book lover, asks the boys to move a bed into the library for her.
When they start school the next day, Ephriam is determined to be popular and show the small-town kids how much a Boston boy knows. He quickly realizes that the curriculum is challenging, the school’s technology is top-of-the-line, and the other students are way ahead of him academically.
Meanwhile, sixth-grader Mallory Green is not happy to hear members of the Appledore family have moved to the castle. Just as the Appledores owned the castle for generations, members of her family have been its servants and caretakers forever. Her father is anxious to help the Appledores, but Mallory just wants to forget about the castle and all the stories her parents have told her about it. Her mother is gone now, having left them yet again. Mom wants Mallory to visit her, but Mallory wishes she could put everything to do with Mom and the Water Castle behind her.
A journal from the early 1900s appears between chapters of this modern tale. It tells the story of Nora, a young black ancestor of Mallory, who goes to work for 97-year-old Orlando Appledore. He’s heard about the girl’s intelligence and asks her to come live at the castle as his assistant. Harry, Orlando’s great nephew, is about Nora’s age. While Harry is away at boarding school, Nora and Harry correspond to discuss the news they read about a team making a groundbreaking Arctic exploration.
Ephriam grows increasingly unhappy when his lack of knowledge at school makes him look foolish. He’s also been instructed to work on his explorer research project with a boy named Will Wylie, who clearly doesn’t like him. He learns that Will’s ancestors were competitors of the Appledores. The Wylies actually claimed they found the healing water first. Generations of Wylies, including Will’s own father, still harbor bitterness against the Appledores. Many believed the Wylies were responsible for a fire that destroyed part of the Appledores’ property in 1909. The explorers that Ephriam and Will are assigned to research are the same men Nora and Harry are following in the old journal entries. Mallory, too, is assigned one of these Arctic explorers.
In science class one day, a teacher brings a Geiger counter. It shows the kids in the class have high levels of radiation, with Ephriam being highest of all. Ephriam begins to wonder if radiation has anything to do with the supposed healing power of the water on his property. He and his siblings have noticed that the house seems alive. They can always feel it humming. They’ve also seen strange flashes of light on occasion. They’ve even found an old bottle with a label saying it contains certified radioactive water. When Brynn finds old house plans and a guest book, they discover that famous scientists visited the Water Castle. They also learn about a series of secret tunnels.
The kids find an old photograph with a girl who is the spitting image of Mallory. When Ephriam shows her the picture, she’s perplexed. Mallory reluctantly shares her parents’ stories about the Water Castle with Ephriam, though she’s afraid he will develop the false hope that the water can heal his dad. When Ephriam mentions the tunnels under the house, Will admits to knowing how to gain access to them through a hidden entrance in a park.
Mallory, Ephriam and Will go through this entrance and find a secret sculpture garden. Ephriam can’t stop thinking about the tunnels, and Mallory finds a logbook written by Nora Darling that proves Appledore’s research on water was progressing. The kids are determined to find Appledore’s secret lab somewhere in the system of tunnels. On their next trek through the tunnels, they find a door with a keyhole.
Mallory knows her mother wears a key around her neck, and she thinks it may be the one that will open the secret door. Even though she’s still hesitant to see her mom, she makes the sacrifice in order to get the key. The kids are able to get into Appledore’s lab, where they find more old bottles of Appledore’s special water.
Ephriam makes sure to leave the door open a crack so he can get into the lab during the night and get some of the water. He drinks it himself and decides that, if it doesn’t kill him by morning, he will give it to his father. Ephriam finally gives his dad the water. As Dad is sputtering and choking on it, Mom walks in and demands to know what Ephriam is doing. Ephriam’s siblings are upset with him for making things worse on the family.
Mallory continues to work through the logbook she’s found. She reads a perplexing statement about the necessity of burning the water. She also comes to believe Appledore had discovered a new element not on the periodic table. She returns to the lab to investigate. Meanwhile, Will and Ephriam have also returned to the tunnels. Ephriam told Will about some high, winding stairs he’d found, and he takes Will to see them.
A stair breaks, and the boys fall a great distance. Mallory is on the roof of the castle when Price and Brynn find her. She tells them that, while she doesn’t understand it all, she believes Appledore’s new element plus radiation may have something to do with the power of the Crystal Springs water. She further suggests that the frame of the house, made of metal, may serve as a conductor. Appledore may have burned water in a tank she saw on the roof to increase its power. They hear the boys’ screams from the fall and run to investigate.
Ephriam is slightly injured, but Will has a large piece of wood jabbed through his thigh. Ephriam isn’t sure what to do for his friend, who is rapidly losing blood. He finds a bottle of Dr. Appledore’s water. Although he still has no idea whether it does anything at all, or whether it could actually make someone immortal, he decides to take the risk and give some to Will. The other kids arrive. They inform him that their mother isn’t home to help.
They carefully move Will to the family’s SUV, and Price does his best to drive it to the emergency room. Sometime later, a doctor tells Will it is miraculous that he didn’t sustain worse injuries. Mallory tells Ephriam that the water saved Will. Having seen no healing in his own father, Ephriam argues that he’s not going to believe in the water anymore.
Mallory talks to her mother, who has been planning a trip to Alaska. She tells Mallory she wants to wait until summer so Mallory can join her. This is a step in rebuilding Mallory’s trust.
Many questions remain unanswered as the story’s ends. What happened to Dr. Appledore? Are Harry and Nora, of the old journals, actually Mallory’s parents, who drank the water and attained eternal life? Did the Wylies burn the Appledore property? Which explorers reached the Arctic first? Was the water powerful due to an amazing scientific discovery, or was it magical? In the final scene, Ephriam is walking near his house and looks up into Dad’s window. He’s shocked to see his father standing at the window and waving at him.