Hazel and Fiver, two rabbits less than a year old and small for their age, are out nibbling grass at sunset. Hazel has a keen mind and the hope of gaining more weight and joining the Owsla, the rabbit police force. Fiver, however, is a runt, considered odd by many in the warren.
When the two come across a sign in a field, Fiver becomes distraught. Hazel has learned to trust his friend’s premonitions of danger, but hopes that this one will pass. When Fiver dreams of bad things happening, Hazel takes him to talk to the Chief Rabbit. He is condescending to Fiver’s fears and sends them away. He then cuffs Bigwig, the member of his Owsla who allowed them to speak to him.
Hazel decides it would be best to follow Fiver’s advice and leave the warren. Even if nothing terrible is going to happen, the warren is crowded, and they would be better off on their own. They gather a few more rabbits including Bigwig and Silver, who are members of the Owsla, along with Pipkin, who is another runt, Dandelion and Blackberry.
Bigwig must fight Capt. Holly, the head of the Owsla, before the group can leave. The intrepid rabbits head off without a set destination in mind. The way is hard, and the group must cross roads that are infested with hrududil, man-made creatures that move quickly and make a lot of noise. Some of the rabbits want to return to the warren, but Bigwig convinces them to stay. Others wonder where they are heading. When they find a good field, Hazel hopes it will be their new home. Fiver, in a trance, tells them they must journey farther. There will be difficulty ahead, but they are looking for a safe place up on a hill.
Hazel and his friends meet another rabbit named Cowslip. Large and fat, Cowslip convinces them to come to his warren. It is big with lots of tunnels and a huge underground room where all the rabbits can congregate together. At first Hazel and his friends are thrilled at their good luck. The new rabbits are friendly, and there is plenty of food. Soon, however, they begin to worry. Fiver will not even come into the new warren, preferring to stay outside in the rain.
Then Hazel notices that the new rabbits will not answer any question beginning with the word “where.” When Bigwig gets caught in a snare, the new rabbits’ motives become clear. A nearby farmer allows them to live unmolested near his farm, even feeding them from his garden, so that he can then trap and kill them. Hazel and his friends free Bigwig and make plans to set off again. Strawberry, one of the new rabbits, is given permission to join their group.
After several days, they come to Watership Down. Hazel and Dandelion explore the top of the hill and find it to be a perfect place for their new warren. From there, they will be able to see all around them and have warning of any enemies in the area. They also find several old rabbit burrows to use for temporary housing. Although warren building is usually done by female rabbits, Hazel and his friends learn to dig themselves. They also borrow the idea of creating a large common hall from Strawberry’s old warren. They are shocked when Capt. Holly and another rabbit arrive, beaten and weary. After resting, Capt. Holly tells the terrifying tale of how Fiver had been correct. Men came and gassed their old home. Then a great machine came and plowed the earth up, destroying everything in its path.
Hazel continues to seek new ways to help himself and the others survive. One morning, he rescues a mouse from a falcon and lets the tiny creature take refuge in one of their tunnels. When it is safe for him to leave, the mouse promises to one day return the favor. Hazel explains to Bigwig and the others that this area is new to them and if they could make friends with other animals, they might be able to learn more about their new home. The tactic pays off when another mouse leads them to good feeding grass. The next day, Bigwig finds a large injured bird unlike any they have seen before. Hazel convinces the bird to take shelter in the mouth of one of their tunnels and then orders the other rabbits to find bugs and worms for it to eat.
This bird is a gull neamed Kehaar, who was attacked by a cat. He and Bigwig become friends as the bird’s wing mends. When Kehaar is ready to fly again, Hazel asks him to fly over the area and let them know if there are any other rabbits near the Down. Hazel is especially interested to learn if there are any female rabbits, as their warren will not survive without them.
Kehaar informs them that there are several rabbits being kept in a hutch on a nearby farm. There is also a large warren located about two days’ journey from them. Holly, Strawberry and two other rabbits are sent as emissaries to the new warren to ask if they might be willing to give up a few of their does. Hazel, wanting to do something useful while they are gone, decides to see if the farm rabbits would be willing to come live at Watership Down. Although they have always been captive, the new rabbits are intrigued by the thought of living free. Hazel promises to return soon and help them escape.
That night, Fiver argues with Hazel, telling him that the venture is foolhardy and hazardous. Hazel promises he will lead Bigwig and several others down to the farm, but will stay out of danger himself. All goes according to plan except that two of the four farm rabbits are too timid to move quickly once they are out of their hutch. Hazel sends Bigwig on with the two farm rabbits named Boxwood and Clover, while he tries to help the other two. The farmer drives up in his car, paralyzing the rabbits with his headlights. He grabs one of the hutch rabbits, allowing Hazel and the other to escape into the brush.
But then Hazel runs out, creating a distraction, and is shot in the leg. He hobbles off and hides in a drainage ditch. His friends believe he has been killed. They set off with heavy hearts toward home. When they get back, they must tell the others of the loss of Hazel. More bad news arrives when Holly and the other emissaries arrive back without any does.
Fiver has a dream in which he sees where Hazel is hiding. The following morning he convinces Blackberry to take him to the farm. They find Hazel in the ditch and slowly start helping him home. Meanwhile, Holly tells the others about the warren, called Efrafa, that they contacted. Although the warren was overcrowded, they would not allow anyone to leave. In fact, Holly and his companions were taken prisoner by Capt. Campion, General Woundwort and the other rabbits of Efrafa.
The group managed to flee and escaped capture when a train prevented their pursuers from following them. Blackberry arrives to tell them that Hazel is alive. Bigwig helps their leader back to the warren. Kehaar picks out shotgun pellets from Hazel’s wound so it will heal.
The following day, Hazel insists they return to Efrafa to bring back does. He assigns Blackberry the task of coming up with a plan, as he has already proven his genius in the past. Fiver agrees that the plan is necessary, and he wants to accompany the group. Hazel asks for Kehaar’s help to bring does back from the other warren. The bird agrees, but says he must leave to find the big water once the job is done.
Kehaar leads the rabbits to Efrafa and helps them to find places to hide from General Woundwort and his patrols. Kehaar also shows the rabbits a boat on a nearby river. Blackberry and Hazel agree that they can use the boat to escape from the patrols once they have freed the does. Bigwig approaches Efrafa, pretending to be a lone rabbit hoping to join the Owsla. With his strength and cunning, he gets a job as an officer. He finds a doe that agrees to get several of her friends to break out of Efrafa and flee with him. They plan on escaping the following night. He alerts Kehaar to tell Hazel and the other rabbits.
Bigwig and the does narrowly escape General Woundwort, Capt. Campion and their soldiers. It is only with the help of Kehaar, attacking their pursuers from the sky, and the blessing of a torrential rainstorm, that they manage to get free. They meet up with the others and use the boat to float away from their enemies. They lose one of the does on the long journey home, but manage to bring 10 females back to their warren.
General Woundwort is not forgiving, however, and he takes time to locate Hazel’s warren and plan an attack. Warned by the little mouse that Hazel had saved earlier, Hazel fills in all but one of the tunnels to their warren. While Bigwig provides protection at home, Hazel, Dandelion and Blackberry return to the farm with a plan to free the large dog that lives there. Just as Hazel chews through its leash, he is attacked by the farm’s cat. Dandelion and Blackberry lead the dog up to Watership Down where Bigwig is valiantly holding off General Woundwort. The general tells his men to stay and fight, but at the sight of the dog, they dash off into the night. Woundwort is never seen again.
Capt. Campion retreats with most of the soldiers from Efrafa. Several surrender and are accepted into Hazel’s warren. Lucy, the little girl on the farm, saves Hazel from her cat. After getting him checked out by a vet, she releases him to the wild at the base of Watership Down.
When fall arrives, the community is pleased to welcome several litters of new rabbits from the does they freed. Hazel plans to help found a new warren between Efrafa and Watership Down to allow both populations to prosper and grow.
Bigwig has become a legend and thrills the younger rabbits with tales of his battles and adventures. In an epilogue, Hazel has lived much longer than the average rabbit. One morning, a rabbit with shining ears comes for him. Hazel leaves his body behind and looks back at the thriving warren he helped to create. Content, he follows his rabbit guide to a new world.