Watership Down is the tale of a group of rabbits in search of a home. Fiver, a small, young rabbit, has a gift: He can tell when things are going to happen and he can sense whether they will be good or bad. Fiver foresees great danger to the rabbits' home warren. His brother Hazel, who is slightly larger and helps take care of Fiver, takes Fiver to the Chief Rabbit, the Threarah. Fiver tells the Threarah that he foresees great danger, but the Chief Rabbit does not believe him.
Hazel decides that they must leave the warren, so he recruits two of his friends, Dandelion and Blackberry, and Pipkin, a friend of Fiver. Bigwig, one of the leading members of the warren (the Owsla), believes Fiver and wants to go with them. They decide to try to convince other rabbits to come; Silver, Buckthorn, Hawkbit, Speedwell, and Acorn all go with them. Hazel is their leader, and he takes advice from Fiver about where to go.
The rabbits go through several adventures before Hazel successfully brings them to a field where they believe they can live. But the field is already inhabited by a group of rabbits, who seem strange but let the travelers stay with them. Fiver warns the rabbits not to join the new warren, but they do not listen to him because the living is easy and there is food for everyone. There is something odd about the warren, but they cannot figure out what it is. Finally, after an argument with Fiver, Bigwig gets caught in a snare. Hazel and the other rabbits manage to get him out, although they get no help from the rabbits who live in the warren. Fiver figures it all out, explaining to the group that a farmer leaves the great food behind for the rabbits in order to fatten them up before he catches them in his snares. They decide to leave, and one rabbit from the new warren, Strawberry, comes with them.
The rabbits travel on until they reach Watership Down. At the top there is a perfect field for a rabbit warren. They settle down in the field, but then Hazel realizes that they need does (female rabbits) to mate with, as they have only bucks and their warren will not last long without does. Holly and Bluebell, two survivors from their home warren, find the rabbits and tell them of a horrible poisoning that occurred. The rabbits befriend a wounded bird, Kehaar, and after he heals he searches for other warrens so they can get some does.
Kehaar finds a warren a few days away, as well as some rabbits living in the farm next to the down. The rabbits send an expedition to the warren (Efrafa) to try to bring back some does, and Hazel sets up a raid to free the rabbits in the farm. The get three of the four rabbits out, although Hazel is badly injured and thought dead until Fiver goes back and saves him. The expedition comes back roughed up, describing Efrafa as a horrible warren run by a militaristic warlord, General Woundwort.
Hazel decides that they must go to Efrafa and get some does, because otherwise they will not survive. He has Blackberry come up with a plan, and then the group sets off, leaving behind a few rabbits at the warren. Along with Blackberry, they sneak to a hiding place close to Efrafa, at which time Bigwig enters the warren, pretending to be a solitary rabbit. He finds a doe, Hyzenthlay, who helps him set up a plan to escape. With the help of Kehaar and his own strength and cunning, Bigwig engineers a masterful escape, and the whole groups flees on a boat just as General Woundwort is about to attack them. However, on the way back to Watership Down, a patrol from Efrafa bumps into them, and Captain Campion tracks them and finds their warren. Soon after they return, a mouse whom Hazel had earlier saved brings him news that there is a large number of rabbits close by. They realize that the Efrafans have brought a large force to destroy them.
Hazel immediately sets the rabbits to work preparing to defend the warren. They bury themselves in and prepare to fight off the invaders, even though they know it will likely cost them their lives. Hazel gets a flash of inspiration and runs off with Dandelion and Blackberry to try to release the dog from the farmhouse and get him to attack the Efrafan rabbits. Meanwhile, Bigwig faces Woundwort in a tremendous battle. Woundwort is bigger and stronger than any other rabbit, but Bigwig defeats him, and soon afterward the dog comes and scatters the Efrafan forces. A cat catches Hazel, but the girl who lives at the farm saves the rabbit and lets him go.
The rabbits live happily in their warren and Campion returns to run the Efrafan warren. They decide to build a third warren halfway between the two and fill it with rabbits from each warren. Hazel lives several years, longer than most rabbits live, and he sees the warren prosper and thrive before he dies.