Although there are many deaths mentioned among Nat's sailing friends and family relations, including his mother, grandmother, brothers, wife, and even his first partner in a sailing venture, the cause of the demise of his father, Habbakuk, is never mentioned directly.
Instead, the book gradually reveals the sad fate of the hopeful and somewhat prosperous man who had risen to captain a ship and wrecked her and her cargo on a shoal during a storm when the windward anchor gave way. After this, Nat's father was said to have "lost his tuck," meaning that he lost his old confidence and never returned to sea. He also lost his accumulated capital and turned cooper to support his family.
After Habbakuk's wife died, his old mother said that he had "lost his windward anchor." She apparently understood that his wife was the last anchor holding him to this life of hardship, and we are led by this to surmise that he died of grief not long after his wife's death.