Zia is a 14-year-old Nicoleño girl living at the Santa Barbara Mission under Spanish colonial rule. Born to an Indigenous mother and a Spanish father, she relocated to the Mission after her mother's death from an illness brought by settlers. She maintains a connection to her heritage by practicing traditional gathering and secretly preparing a salvaged boat, hoping to cross the dangerous sea channel to locate her lost aunt on the Island of the Blue Dolphins.

Karana is a Nicoleño woman and Zia's aunt who survives entirely alone on her ancestral island for years after her tribe's forced relocation. She possesses profound survival skills and a deep bond with the natural world, retaining the traditional language and customs of her people. Her isolation makes her entirely unfamiliar with Spanish colonial practices and Mission life.

Mando is Zia's younger brother, an Indigenous boy living at the Santa Barbara Mission. Disconnected from his cultural history, he focuses largely on practical skills like fishing and carving oars. He views the discovery of the boat as an opportunity for personal advancement, taking pride in his ability to navigate the physical challenges of their world.

Stone Hands, known in Spanish as Gito Cruz, is an Indigenous man from a northern tribe who serves as a steward at the Santa Barbara Mission. He possesses strong political awareness and deeply resents the unpaid labor forced upon his people. Utilizing his influence among the workers, he organizes secret meetings to plan escapes and resist the colonial authorities.

Father Vicente is a young, thin Catholic priest stationed at the Santa Barbara Mission. Unlike many of his peers, he shows genuine compassion for the Indigenous population, attempting to reform the system from within by establishing fairer labor laws. He frequently places himself between the vulnerable Mission residents and the violent military garrison.

Captain Cordova is the head of the military garrison that oversees the Santa Barbara Mission. He enforces colonial rule with threats, suspicion, and physical intimidation. Viewing the Indigenous population strictly as laborers or criminals, he uses his authority to bypass the church's jurisdiction whenever he suspects rebellion.

Captain Nidever is a white trader, sea otter hunter, and skilled sailor who navigates the waters off the California coast. He is pragmatic and well-aware of the ocean's extreme dangers, leading him to doubt the children's ability to cross the channel in a small boat.

Father Merced is an older priest who oversees the daily operations of the Santa Barbara Mission. He enforces the strict, exhausting work schedules demanded by the colonial system but holds some protective instincts over his parishioners, occasionally attempting to shield them from the outright violence of the military garrison.

Father Malatesta is a rigid, unyielding priest appointed to lead the Santa Barbara Mission. He firmly believes in the harsh enforcement of assimilation policies and forced labor, viewing the Indigenous residents strictly as a workforce meant to improve the Mission's wealth. He quickly abolishes any lenient practices established by his predecessors.

Señora Gomez serves as the warden of the military prison where dissenters are held. She follows orders efficiently, managing the grim environment of the mud-floored cells without offering any overt sympathy or comfort to the captives.

Rontu-Aru is a dog who serves as Karana's loyal companion. Brought from the island to the mainland, he acts as her constant protector. Accustomed to the wild, he outright rejects the rigid structures of the Mission, preferring to sleep outside in the courtyard.