The protagonist of the series, Bonobono, is a young sea otter who resides with his father by the ocean, near the edge of a forest. His name was given to him by his father, inspired by the sound of a stone dropping into the sea. He is seldom seen without a shellfish in his hand, which he carries as an emergency food source, a habit reflecting the real-life behavior of sea otters who store stones and shells under their arms.

In terms of personality, Bonobono is defined by his innocent, gentle, and warm-hearted nature. His actions are characteristically slow, and his manner of speaking is often vague and meandering, a trait he shares with his father. He possesses a unique and curious way of thinking, which frequently becomes the engine for the story's events as he and his friends explore the simple, everyday mysteries that capture his attention, such as the nature of clouds or the purpose of sleep. This curiosity, combined with his slow movements, often makes him the target of frustration from his more irritable friend, Araiguma.

While his persona is typically calm, Bonobono is prone to small worries that spiral into wild, imaginative anxieties. A regular subject of these fears is the Cave Man, or Putaway Man, a frightening imaginary entity that he conjures up to threaten him with confinement in a cave for various perceived misdeeds. In the earlier iterations of the story, it was extremely rare for him to show anger, but as the series progressed, his character developed to more frequently express frustration and act as a straight man to his friends' absurdities.

Bonobono's primary motivation is his simple desire to understand the world around him and navigate his daily life and friendships. His role in the narrative is that of a gentle, curious observer whose innocent questions lead to philosophical, and often humorous, explorations of life's small truths. His key relationships include his father, who raises him alone following the death of Bonobono's mother shortly after his birth. He is close friends with Shimarisu, a timid and skittish chipmunk, and Araiguma, a short-tempered raccoon who often tries to keep the other two in line. He also shares a bond with Sunadori Neko, a sensible fishing cat who often serves as a source of answers for the group.

Regarding notable abilities, Bonobono is a strong swimmer and diver, which is natural for his species. Despite his generally slow and gentle demeanor, he has displayed surprising bursts of strength in moments of distress or altered mental state, such as when he once ate a poisonous mushroom and became aggressive, or when he single-handedly held a rope to prevent his father from falling. However, he is comparatively slow and clumsy on land, and he is notably unable to catch fish, relying on his father for that part of their diet.