The main character is Edward Sanders, an English medical doctor, who arrives to the river port of Port Matarre, in Gabon. From here he tries to reach a leprosy treatment facility where his friends, Max and Suzanne Clair, live. Soon, however, he starts to recognize that a mysterious phenomenon is crystallizing the jungle along with its living creatures. The same phenomenon is reported to be present also in the Floridaeverglades and in the Pripyat Marshes (Soviet Union) as well. Scientific explanations of the phenomenon are provided within the book: however, Ballard offers mostly an interior and psychological perspective about it, directly through Sanders' experiences. Several facts, furthermore, remains unexplained: for example, the ability of jewels to liquefy the crystals. The crystals also have the property to keep objects and beings in a suspended state of existence. Many passages deal with this characteristic, pointing out its capability to stop time and life.

In his route towards the deep of the forest, Sanders gets involved in a personal feud between Ventress, a Belgian architect, and Thorensen, the director of a diamond mine. In one of the most striking episodes of the novel, Sanders discovers the reason of the deadly rivalry to be Ventress' former wife, Serena, who is terminally ill with tuberculosis. After a final confrontation, Thorensen decides to remain in his house within the jungle, in spite of the encroaching crystallization process. Two of the other characters met by Sanders in his voyage spontaneously make the same decision: Balthus, an apostate priest, and Suzanne. The latter, nearly gone mad and sporting the first symptoms of leprosy, is portrayed towards the end of the novel as the leader of a band of lepers who set for the interior of the crystallizing forest, clearly to never come back.
After having barely escaped from the now quickly spreading crystallization, Sanders reaches Port Matarre. Here, however, he makes the same decision as Balthus and Suzanne. In the final pages, Sanders goes back to river to face the same fate as Suzanne.