The story resembles the tale of Captain Ahab in Herman Melville's Moby-Dick, who was also on the deck of a wooden ship searching for a white whale.

Pawana is about the discovery of a lagoon in Mexico at the end of the 19th century where gray whales went to reproduce.

After Captain Scammon mistakenly decided to exterminate the whales, he realized that he had made a mistake so terrible it could become irreparable.

Captain Scammon then set about dedicating his life's work to saving these whales (and was helped by a Mexican revolutionary in doing so).

John, the eighteen-year-old cabin boy and Captain Scammon alternate in recounting a journey.