Richard Hugo, an excellent poet and teacher, said that each poem has two subjects - the triggering subject (or the story), and the second, deeper subject. This holds true for many great works of literature, not just poems, and The Sound of Waves is no exception.
On the surface, we have a subtly erotic love story about Shinji and Hatsue, two hard-working young Japanese people in a close-knit, isolated, traditional village. They go on with their romance despite ugly rumors which prompt Hatsue's father, Terukichi (known as "Uncle Teru") to forbid his daughter from seeing Shinji. There is a happy ending, but I won't give it away.
This is more than your typical love story. The main characters, Shinji and Hatsue, are ideal Japanese people in the traditional, uncorrupted village: hard-working, devoted to the family, honest, and religious. The rumormongers are Westernized: Chiyoko - a pessimistic girl - is a student in western literature at a city university, and Yasuo - a rude, selfish, lazy boy who wants Hatsue for himself - is well-read in pulp magazines. It is traditional Japanese willpower and discipline that keeps Shinji and Hatsue together despite their obstacles.
What is remarkable is that the book does not make its point with a sledgehammer. The traditional characters win out, not because they tattle or scream; their integrity forces the modern characters to face the errors of their modern ways. This book is almost as relavent to our changing America as it was to Mishima's changing Japan. One read-through and you will understand Mishima's patriotism, his long quest for a return to tradition that led to his seppuku.