The Sound of Waves is a story of first love and coming of age set in the post-WWII years on the Japanese island of Uta-jima. The protagonist is Shinji, an eighteen-year old young man of great physical strength, courage, kindness, and fresh-faced naiveté. He lives with his mother and younger brother on the island, a small, isolated, and beautiful locale that the modern world has barely encroached upon. Shinji is a fisherman on a ship owned by Jukichi Oyama, the Taihei-maru, and his life's goal is to own his own boat with his brother and fish the waters he knows and loves so well off Uta-jima.
When the novel begins, Shinji returns from a day at sea and notices a girl he has never seen before on the beach. He is immediately entranced by her natural beauty and gracefulness, and wonders at her identity. The next day out at sea, he finally hears from Jukichi that the girl is Hatsue, the daughter of the island's richest man, Terukichi Miyata. Terukichi has brought her home after many years away working as a diving girl living with another family, because his only son has died and he is lonely. This information stirs something within Shinji, who has never before been aware of the unknown world outside of Uta-jima.
At a meeting of the Young Men's Association, the communal gathering of the island's young single men, Hatsue's name is further mentioned, along with the news that the YMA's leader, a rich young braggart named Yasuo, is to marry Hatsue. A few days later Shinji and Hatsue meet for the first time while he is climbing up near a ruined tower on an errand for his mother. He hears someone crying, and on investigating finds Hatsue, weeping because she is lost. Shinji helps her along her way to the lighthouse and the two agree to keep their meeting secret from the gossipy village denizens.
Shinji and Hatsue meet at the beach the next day, their mutual attraction becoming more apparent. Hatsue explains that she has no plans to marry Yasuo, and, a few moments later, they kiss as if compelled by some external influence.
Shinji and Hatsue plan another meeting at the tower, as they are falling deeper in love. While in the ruins of the tower they come very near to losing their virginity to each other, but Hatsue stops this, saying it would be morally wrong and that she wants to wait until she and Shinji are married. Shinji is ecstatic that she wants to marry him and agrees to wait. Chiyoko, the lighthouse keeper’s daughter now home from studying in Tokyo, observes them on their way down the mountain. Distraught because she has feelings for Shinji and deep insecurities about her looks, she spreads this information to Yasuo, who burns with jealousy and rage at his slighted pride. He conceives of a plan to rape Hatsue when she goes to draw water from the well late at night, but she is saved from his attempt when a hornet repeatedly stings Yasuo, giving her a chance to escape.
The rumors concerning Shinji and Hatsue began swirling around the island and soon reach the ears of Terukichi Miyata, Hatsue's father. Enraged at his daughter's actions and the disparity between the lovers' social classes, he forbids Hatsue from seeing Shinji. The lovers begin exchanging secret letters, ferried back and forth by Ryuji. Chiyoko begins to feel a sense of remorse for the estrangement that she has created, and goes to apologize to Shinji before returning to Tokyo. Once in front of him, she is too nervous to apologize and tell him the truth, but instead blurts out a question –"Am I ugly?" Confused, Shinji truthfully answers that she is indeed pretty, leaving Chiyoko elated and determined to find a way to atone for her earlier actions.
Shinji and Hatsue attempt to meet late one night but are foiled by her father again. Shinji's mother endeavors to rectify the situation by marching to Terukichi's home and asking him to allow the children to marry, but he refuses to see her, and she shouts at him, only making things worse.
One day the captain of the Utajima-maru, one of the Terukichi's large coastal freighters, comes to the island and invites Shinji and Yasuo to apprentice on the ship as rice-rinsers. Shinji proves his mettle on the ship, while Yasuo is revealed to be lazy, apathetic, and insubordinate. One day amidst a raging storm, Shinji risks his life to dive into the heaving sea to tie the ship back to a buoy. This courageous act earns him the esteem of the captain, and later, Terukichi.
When the ship returns, Shinji waits to hear news of Hatsue. Chiyoko confesses to her mother in a letter, and says she will not return to the island until things are made right between the young lovers. Her mother, along with a few other diving women who adore Hatsue, go to Terukichi's home and ask him about the lovers' future together. To their surprise, he explains that he has already decided to allow Shinji and Hatsue to become engaged, and to marry once they are a little older. He says he has realized that wealth and background are not as important as a man's "get-up-and-go," and that the island needs more men like Shinji.
The novel closes with Shinji and Hatsue reveling in their love and engagement, and visiting the lighthouse to look out upon the sea.