Watership Down opens with a narrated prologue establishing the Lapine culture and mythology, describing the creation of the world and its animals by the sun god "Lord Frith," including the rabbits' leader, Prince "El-ahrairah." All the animals are friendly, and eat grass, but the rabbits soon multiply and overwhelm the other animals. When Frith warns El-ahrairah to control his people, the prince scoffs at his warning; in retaliation, Frith gives each animal a gift, turning them into predators that hunt down and kill the rabbits. However, Frith also gifts the rabbits, with speed and cunning; all creatures may seek to kill El-ahriarah and his descendants, but the rabbits may survive by their wits and their quickness. The film then switches from a stylized narrative to realistic animation, set in the English countryside of Sandleford. Fiver, a young runt rabbit with prophetic abilities, foresees the end of his peaceful rabbit warren and asks others to leave with him. Fiver and his older brother Hazel attempt to persuade their Chief Rabbit to have the warren evacuated and moved elsewhere, but they are dismissed, and attempt to recruit individuals instead. The group meets resistance from the warren's police force, or Owsla, but eight manage to fight and escape: Fiver, Hazel, the burly ex-Owsla officer Bigwig, the cunning Blackberry, the smallest rabbit Pipkin, storyteller and runner Dandelion, the elder Silver, and the only female, Violet.
They travel stealthily through the woods, close to many predators, but make it to a covered bean field to rest the night; however, in the morning, as she attempts to feed nearby, Violet is killed by a hawk. After crossing a road and a river (using a floating piece of driftwood), evading a hunting dog, and escaping from a rat-infested cemetery, the hungry band meets a rabbit named Cowslip, who invites them for much-needed food to his warren of strange but friendly rabbits. The group is content and grateful for shelter, but Fiver senses something terribly wrong and leaves in a fit. As Bigwig follows him, taunting his bizarre behavior, he is caught in a snare; Fiver attempts to get help from Cowslip and his warren, but he is dismissed. As the rabbits frantically dig to free Bigwig, he collapses. As the rabbits mourn him, Fiver admonishes them: The warren is fed by a farmer who occasionally snares rabbits in return for his food and care from predators. After this revelation, Bigwig miraculously awakes; on Fiver's advice, the band moves on with new respect for the seer's wisdom.
The rabbits discover Nuthanger farm, which contains a hutch of female rabbits. Hazel realizes that females will be needed to begin a new warren, but the rabbits are forced to leave by the appearance of the farm's cat and dog. Hazel promises to return, and the rabbits set off again. They are unexpectedly found by the Sandleford's Owsla Captain, Holly, who is injured and at the point of death. He recounts the destruction of the Sandleford warren that Fiver foresaw, and collapses after mentioning a warren called Efrafa. After he recovers, Fiver soon leads the group to the high hill he envisioned, Watership Down, where the rabbits discover empty burrows suitable to live in. They settle in, developing their own warren, with Hazel informally recognized as Chief Rabbit.
They befriend an acerbic injured seagull, Kehaar, who offers to survey the local area for females. Meanwhile, the rabbits return to Nut hanger farm to free the does, but as they make their escape, Hazel is shot by a farmhand and presumed dead; however, Fiver, following a vision, returns to the farm to discover Hazel still alive. Kehaar returns, and while removing buckshot pellets from Hazel's leg, reports of Efrafa, a large warren which may have females. Holly, who knows of Efrafa, begs them not to go there, describing it as a highly militarized and totalitarian state; however, Hazel, fresh from his injury, feels they have no choice but to seek does there.
Bigwig decides to infiltrate the colony: He impresses the Chief Rabbit, the powerful General Woundwort, who makes him an Owsla officer. In time, Bigwig recruits several would-be escapees to his cause, including Hyzenthlay, an outspoken, rebellious doe, and Blackavar, a persistently attempted escapee permanently scarred as a public deterrent. After one morning's feeding (or silflay), they escape, with Woundwort and the Efrafan Owsla in hot pursuit. Aided by a timely airborne attack by Kehaar during a lightning storm and their use of a boat off a river bank (echoing their earlier use of driftwood), the group barely escapes.
However, their union is short-lived: Efrafan trackers discover their trail several days later, following them to Watership Down and laying siege upon the warren, with the General himself planning to recapture the escapees. Hazel escapes to confront and reason with Woundwort while he's still in Efrafa, offering an alliance of "free and independent warrens"; after appearing surprisingly intrigued, Woundwort abruptly dismisses him, ordering Hazel to "tell Bigwig" to unconditionally surrender. It is then that Hazel decides to fight: Upon his return, the Watership rabbits hole themselves up inside their own warren, and are soon besieged by the Efrafans. In all the commotion, Fiver slips into a trance, in which he envisions "a dog loose in the woods" from their earlier travels. His moans scare the Efrafans, but inspire Hazel: to free the dog from Nuthanger and lead him to the warren to attack them. He again escapes, this time with several rabbits, whom Woundwort ignores, intent on finding Bigwig.
On their way, Hazel prays to Frith, offering his life for the life of the warren, a bargain Frith reveals he cannot bequeath. Upon their arrival, Hazel proceeds to chew off the dog's leash, after which he is pounced on by the cat, but is rescued by the farmer's daughter. His companions, chosen for their running ability, bait the dog in relay fashion into following them uphill to Watership Down. When the Efrafans finally break through the warren's defenses, Woundwort jumps in first; Blackavar attacks him, but Woundwort easily overwhelms and kills him. Woundwort is soon ambushed by Bigwig, and the two fight to near exhaustion; when Woundwort asks why he won't surrender, Bigwig defies him: "My chief's told me to defend this run." Woundwort, who had always assumed Bigwig was chief, hesitates as he imagines a rabbit even larger than the formidable Bigwig in charge of the warren.
As he wonders, the farm dog arrives, led to the warren by Hyzenthlay; the dog goes into a blood-rage and quickly kills the Efrafan rabbits standing guard outside the warren. Hearing their screams, the General abandons Bigwig and emerges from the warren; as the dog sees him, he runs to attack Woundwort, who in turn fearlessly leaps to confront the dog. Later, no trace of the General is found, and his memory becomes a ghost story used by rabbit parents to frighten their children into obedience. The rabbits of Watership Down are safe at last. The epilogue shows the thriving warren several years later. As stories are told of the warren's early exploits, a tired, elderly Hazel attempts to silflay when he is visited by a shadowy rabbit, eventually revealed as Prince El-ahrairah. He invites Hazel to join his Owsla, assuring him of Watership Down's perpetual safety. Reassured, Hazel agrees; he falls asleep on the grass and peacefully passes away. In a reprise of other mystical scenes in the film, Hazel discards his body and freely follows El-ahrairah through the woodland and trees towards the sun—which metamorphoses into Frith—and into the afterlife:
“ All the world will be your enemy, Prince with a Thousand Enemies. And whenever they catch you, they will kill you. But first, they must catch you: digger, listener, runner, prince with the swift warning. Be cunning, and your people will never be destroyed. ”
- John Hurt as Hazel
- Richard Briers as Fiver
- Michael Graham Cox as Bigwig
- John Bennett as Captain Holly
- Ralph Richardson as Chief Rabbit
- Simon Cadell as Blackberry
- Terence Rigby as Silver
- Roy Kinnear as Pipkin
- Richard O'Callaghan as Dandelion
- Denholm Elliott as Cowslip
- Mary Moddox as Clover
- Lynn Farleigh as Tab
- Zero Mostel as Kehaar
- Harry Andrews as General Woundwort
- Nigel Hawthorne as Campion
- Hannah Gordon as Hyzenthlay
- Clifton Jones as Blackavar
- Derek Griffiths as Vervain and Chervil
- Michael Hordern as Lord Frith and Narrator
- Joss Ackland as Black Rabbit of Inlé and El-Ahrairah
- Michelle Price as Lucy
- Joe Ranft as Bob the Dog
- David Hyde Pierce as Toadflax
Music By Angela Morley and Malcolm Williamson
- "Bright Eyes" - Art Garfunkel
- "Bright Eyes" - Mike Batt