Hazel and Fiver are rabbits—and brothers—who live in a warren in Sandleford, in the English countryside. Their warren is a generally happy place, though Hazel and Fiver, who often has strange visions of the future, occasionally have to contend with condescending treatment from their warren’s Owsla, or police-like protectorate. When Fiver sees that a notice has been put up by humans at the edge of the field which houses their warren, he has a vision of the burrow’s destruction. Fiver says that they need to evacuate, but the warren’s Chief Rabbit, the Thearah, dismisses the rabbits out of hand.
That evening, Hazel and Fiver make a plan to leave the warren with couple of friends, including Blackberry and Dandelion. A fearsome member of the Owsla, a rabbit named Bigwig, approaches Hazel and Fiver at their evening meal and tells them he wants to go with them. That night, the rabbits set off along with some new additions—Buckthorn, Silver, Hawkbit, Speedwell, Pipkin, and Acorn—but the captain of the Owsla, Holly, attempts to arrest them. Bigwig fights Holly off, and Hazel offers the rabbit one last chance to come with them. Holly rejects the offer.
The rabbits set out on their journey, frightened by every strange sight, smell, and sound. Hazel falls into the role of leader, and no one contests his natural ability to guide the rabbits to safety. As they travel, the rabbits comfort one another on their journey with tales of the rabbit trickster folk hero, El-ahrairah, and his triumphs against the enemies of rabbits throughout the ages. One afternoon, the rabbits are approached by a stranger named Cowslip who tells the group that he has a warren nearby and invites them to stay for as long as they want. Hazel, knowing the group is in need of a safe place to stay, accepts Cowslip’s invitation, and their group follows him down to his burrow.
Fiver has a bad feeling about the place, but Hazel ignores him. There is something strange about the rabbits in Cowslip’s warren, though—they are all large and healthy-looking but seem sad and fearful. However, Hazel and the others are enticed to remain in the warren after they realize that the rabbits there eat flayrah—delicious food such as lettuces, carrots, and roots—left out by a nearby farmer for nearly every meal.
Fiver again attempts to warn Hazel that something is very wrong, but Hazel continues to ignores his brother’s warnings. Soon Fiver leaves the burrow, planning to run away. Bigwig and Hazel follow him, and Bigwig yells at Fiver for putting his visions above everyone else’s safety. As Bigwig heads back to the warren, he becomes caught in a snare. Fiver goes for help, and together their band of rabbits frees Bigwig. Fiver explains that the rabbits in Cowslip’s warren are fed by the farmer, who only keeps the rabbits big and healthy so that they will be more valuable as pelts and meat. Realizing at last how dire their situation is, Hazel and the others leave—one member of Cowslip’s warren, the kindly Strawberry, joins them.
The following evening, the rabbits arrive at the safe refuge Fiver has seen for them in one of his visions: the tall, verdant hill of Watership Down. Over the next few days rabbits construced their big, happy warren, even building a large common room known as the Honeycomb so that they can spend time together and tell stories in the evening.
One night, at silflay—feeding time—the rabbits hear something coming. They are shocked when they find themselves face to face with the injured Captain Holly and another rabbit from Sandleford, Bluebell. Holly and Bluebell share the story of Sandleford’s destruction, which happened just as Fiver said it would. Men filled in the tunnels with dirt and pumped gas into the burrow before using large machines to dig up the earth. Holly and Bluebell escaped, but not before being traumatized by the carnage all around them. They wandered in the fields for days, following Hazel’s tracks and encountering all manner of elil (predators). Hazel and the others tend to Holly and Bluebell’s wounds and welcome to Watership Down.
The following day, Bigwig and Hazel spot a large white gull in the fields. The bird is wounded, and though he barely speaks the rabbit’s language, Lapine, the rabbits communicate to the bird that he is welcome to stay and rest for as long as he wants. Hazel secretly hopes that he will win the bird’s affection and will be able to ask the bird for a large favor once he’s healed. Hazel knows that because there are no does, or female rabbits, in their group, their warren will cease to exist in just a few years; he wants the bird to fly around and scout out another warren to which they might be able to venture and ask about taking some does back to Watership Down.
Sure enough, as soon as the bird, whose name is Kehaar, has healed up, he offers to help the rabbits find “mudders” to mate with, even though he longs to get back to his own flock. Kehaar flies out and returns a couple of days later, reporting that there is a farm nearby where some rabbits live in a hutch, and also a large warren a two-days’ journey away. Hazel sends Holly, Silver, Buckthorn, and Strawberry out to the other warren, and he himself gets together a band of rabbits to raid the farm. The raid, however, is a disaster. The hutch rabbits barely make it off the farm into the field beyond, and when the owners of the farm see the rabbits loose in the yard, they go after them with torches and guns. Hazel is shot, and the rest of the rabbits are forced to return to Watership Down believing their leader dead. When they get there, they learn that the other search party has returned from the nearby warren with a terrible tale to tell.
Holly tells the story of the journey to Efrafa—an authoritarian, militaristic warren run by the fearsome General Woundwort. Rabbits at Efrafa are bitten at birth on different parts of their bodies, and based on this Mark, are forced to keep to a tight schedule which only allows them above ground once a day. A large Owsla, a Council of officers, and several groups of Mark leaders and sentries—plus Wide Patrol officers which lead scouting missions throughout the fields nearby—see to it that no one ever escapes. Holly and the others barely managed to do so by running away during an evening silflay. They were pursued by a Wide Patrol, but as they crossed an “iron road”—train tracks—they were saved when a train came along and killed the Efrafan officers. After the story is over, the rabbits learn that Fiver and Blackberry have gone to retrieve Hazel after Fiver saw his brother alive but wounded in a vision.
Hazel recovers, though his leg has been weakened considerably. He is grateful to see that the hutch rabbits are settling in nicely, but knows that they will need more does—otherwise, during mating season, there will be fighting. Though Holly has filled Hazel in on the horrors of Efrafa, Hazel knows their group must return there to rescue some does.
Hazel, Blackberry, Bluebell, Dandelion, Pipkin, Fiver, Silver, and Bigwig carefully make their way towards Efrafa. Along the way, rabbits narrowly dodge a fox when Bigwig draws it off into the nearby woods. After several days they make their way to a river. There, the rabbits discuss how best to escape from the Wide Patrol’s clutches after the plan to get does out of Efrafa—which involves Bigwig infiltrating the warren on his own and posing as a wandering hlessi, or wild field rabbit—is complete. Blackberry suggests they use a small wooden boat which is tied up by a rope to the riverbank to float down the river and escape the patrol. Bigwig sets off for Efrafa at once.
In Efrafa, General Woundwort is summoned to meet with a hlessi who has appeared nearby and asked to join the warren. The warren is overcrowded, a group of does have recently asked to leave, and several officers have recently been killed in an encounter with a fox. Feeling his control slipping, Woundwort sees his meeting with the rabbit—who has a tuft of fur on his head and introduces himself as Thlayli, or Bigwig—as a chance to bring in someone strong and new. The Council members appoint Bigwig to the Owsla immediately and give him a Mark to initiate him as an Efrafan.
As Bigwig meets with the other officers and Council members including Chervil, Campion, Aven, and Vervain, he learns how things work in Efrafa and is overwhelmed by the amount of danger he faces. Bigwig learns that a group of does led by the intrepid Hyzenthlay have recently shown signs of rebellion. Taking advance of his “privileges” as an Officer, Bigwig orders a sentry to bring Hyzenthlay to his burrow one night. Once she’s there, he tells her that he wants her help in staging a breakout of several does, plus a badly-mutilated rabbit named Blackavar, who has been made into an example for the other rabbits after a recent escape attempt of his own. Hyzenthlay knows the risks, but dreams of a better life and agrees to help Bigwig. He tells her that tomorrow at the evening silflay, they will make a break for it—a bird, he says, will aid in their escape, and they will meet with the rest of Bigwig’s group at a nearby river.
The following morning, Bigwig finds that a thunderstorm is approaching. At silflay, Bigwig spots Kehaar nearby and tells him that the plan is to be executed that night. When Chervil sees Bigwig standing so near the gull, however, he insists its sighting must be reported, as it isn’t the season for gulls and everything even slightly unusual in Efrafa must be reported at once. After silflay, Bigwig tells Hyzenthlay that the breakout is going to happen at sunset. When Bigwig returns to the field at sunset, though, he is approached by General Woundwort, who asks him about his proximity to the bird earlier and whether he was involved in drawing a fox into a group of Wide Patrol earlier in the week. Bigwig apologizes for his role in the attack, insisting he was simply trying to save his own life. The plan is delayed until the next day, since Bigwig has missed his chance while talking to Woundwort.
The next morning, Bigwig manages both to signal that the plan has been rescheduled for the evening to Kehaar and to warn Blackavar to be ready. That afternoon, Hyzenthlay tells Bigwig that a doe named Nelthilta has been arrested. Hyzenthlay is worried that Nelthilta will give their plan away, and Bigwig hurries to put things into motion early. He manages to deceive the guards, sneak Blackavar away from his captors, and herd the does into the field beyond Efrafa, but soon a group led by Campion catches up to him. Word of Bigwig’s dissent has made it back to Woundwort, and he and several other officers are on their way. When Woundwort at last approaches, Bigwig curses him and his Owsla—at that moment, a great bolt of lightning comes down from the sky, and Kehaar swoops in from nowhere, startling the Efrafan rabbits while Bigwig and the others make their way to the river and onto the boat. Woundwort and the rest of the Efrafans catch up to them, but having never seen a boat before, are not able to stop them.
The rabbits drift downriver on the boat, stunned and traumatized. Soon, they become caught in a bridge’s culvert, and are forced to abandon ship and swim to shore. Having successfully outstripped the Efrafans, the rabbits rest for the night before heading onward the next morning. Over the course of their journey back they are forced to say goodbye to Kehaar, who is returning to his own flock now that his favor to them is complete, and lose a couple of does in run-ins with foxes and other forces of nature. The rabbits are pursued by Campion and a few other Efrafans, but Hazel confronts them and tells them they’re outnumbered. The Efrafans appear to turn around and head back, but in reality, they follow Hazel’s band all the way back to the foot of Watership Down before returning to Efrafa to gather more troops.
Unaware that the Efrafans are plotting against them, Hazel, Bigwig and the others look forward to the birth of new litters and the prosperity of their warren. They share stories of El-ahrairah’s deception of a farmyard dog in pursuit of some cabbages, and marvel at how far their scrappy little band has come. One afternoon, though, a mouse brings news that other rabbits have been spotted in the field. Hazel sends a patrol out, and the rabbits return with word that Campion, Woundwort, and the rest of the Efrafan Council and Owsla are planning to storm Watership Down. Hazel meets with them to beg for peace, but Woundwort will not have it. The rabbits ready Watership Down for a siege, closing up all of the tunnels and runs. When the Efrafans start digging down into the center of the Honeycomb, Hazel has an important “vision” of his own. He scurries from the warren with Dandelion and Blackberry in tow, leaving Bigwig in charge of the defense while he readies one final trick.
Down at Nuthanger Farm, Hazel frees the farmyard dog from his kennel and has Blackberry and Dandelion lead it back to Watership Down—Hazel himself, though, is attacked by a cat. Back at the Down, the Efrafans infiltrate the Honeycomb. Woundwort and Bigwig have a violent confrontation in which Bigwig severely weakens the Efrafan leader. Woundwort retreats above ground and orders his Owsla to dig into the burrows from all sides. Soon, though, a dog rushes up the hill, chases the Efrafans away, and confronts Woundwort, who meets its attack head-on.
The next morning, Hazel is found by a little girl, Lucy, who lives at Nuthanger Farm. She saves him from her cat and nurses him back to health with the help of a country doctor. The two humans drive Hazel out to the fields and release him right at the foot of Watership Down. The Efrafans have retreated, though a couple of them, having surrendered to Bigwig, peacefully begin integrating into life at Watership Down.
Six weeks later, in mid-October, Bigwig and Hyzenthlay have mated, as have Fiver and a doe named Vilthuril. The warren is thriving, new litters are being born all the time, and the rabbits’ days and nights are peaceful. Even the approach of winter does not worry them. They have received news that Efrafa has been reformed under the leadership of Captain Campion, and there is even talk of establishing a new warren at the midway point between the two. In an epilogue, Hazel dies peacefully after a long, happy life, and is summoned from his deathbed to the next world to join the Owsla of his hero, the trickster El-ahrairah.