Nathaniel Bowditch was born into a large family, with six siblings: Hab, William, Sammy, Mary, Lizza, and Lois. He was raised by his parents and his paternal grandmother. His father, who faced significant setbacks in his shipping business, often spent too much time "splicing the main brace," or drinking in local taverns. To help improve the family's financial situation, twelve-year-old Nat became an indentured servant to Ropes and Hodges, a ship chandlery that supplied nautical equipment to merchant ships. The family, pleased to have "one less mouth to feed," sent Nat to live with Mr. Hodges. Instead of the formal education he desired, Nat had to learn by working at the chandlery. Despite discouraging remarks from Ben Meeker, an occasional visitor, Nat educated himself after work by reading and compiling information into notebooks. He maintained separate notebooks for different subjects, recording knowledge from others and his own experiments. This meticulous habit of documenting useful information served Nat well later in life.

"I can do it," Nat roared, "I'm doing it now! If I can teach Lupe to take a lunar, I can do anything!" He paused... Captain Prince stared at him for a count of ten. "Carry on, Mr. Bowditch."
Several characters played significant roles in Nat's self-education. Mr. Ropes allowed him access to an encyclopedia, and Dr. Bentley, a local clergyman, provided him with the use of a private library. Nathan Reed encouraged his scientific experiments, and Sam Smith taught him about sailing. These nautical connections were crucial when Nat went to sea after nine years at the chandlery. Captain John Derby, the owner of several Salem ships, hired Nat to serve under Captain Henry Prince. During his voyages, Nat met many sailors, teaching them navigation. Several, such as Lem Harvey, Zack Selby, and Lupe, became important figures in his life. Other significant characters included Elizabeth Boardman, whom Nat eventually married, and her cousin Mary Ingersoll, known as Polly.

Nat faced the deaths of family members and friends frequently during his early life. His mother and grandmother died when he was twelve, leading to his indenture to Ropes and Hodges. Even before this, his seaman friend Tom Perry died fighting the British. After the accidental death of his favorite sister Lizza, most of the other deaths occurred at sea: Captain Boardman, Nat's brother Sammy, and his brother-in-law David Martin, who died along with his entire crew. Although Lem Harvey was presumed dead, he survived the sinking of his ship. Nat's other brothers, Hab and William, were lost at sea.

These maritime deaths increased the urgency for Nat to complete his book on practical navigation, which could save lives at sea. Additionally, the many losses forced Nat to mature quickly and address personal challenges at a young age.

Persistence, especially the determination to make the best of a difficult situation, is a central theme in the book. Nat has a natural talent with numbers and diligently teaches himself about astronomy, mathematics, sailing, and languages. Creativity and ingenuity are key aspects of Nat's perseverance. For instance, he learns foreign languages by translating from English using a dictionary and a Bible.

Despite others frequently assuring him that things will improve, Nat doesn't just wait passively. He puts in hard work on both assigned and self-initiated tasks. The narrative contrasts other characters' hopeful thinking with Nat's proactive efforts to better a seemingly stagnant situation. Even though his efforts do not yield immediate rewards, he continues to acquire knowledge, anticipating its future usefulness.

An important secondary theme is Nat's passion for teaching. After mastering a subject, he is eager to educate others and documents effective methods for explaining navigation to his fellow sailors. Nat's teaching strategies highlight the significance of clear and simple explanations combined with boundless patience.