Bonobono is the main protagonist, a young male sea otter distinguished by his sky-blue fur. He lives with his father in a home on a cliff by the sea, situated on the edge of a vast forest where he spends most of his days. His mother passed away when he was very young, leaving him to be raised solely by his father.

In terms of personality, Bonobono is defined by his innocent, gentle, and warm-hearted nature. He is, however, slow-witted and has a vague way of speaking, a trait that appears to be hereditary from his father. He is deeply curious about the world around him, which often leads him to ask many questions about how things work or why things happen. This curiosity is the primary driver for many of his daily adventures and conversations with his friends. Despite his kind disposition, he can become frustrated, though his expressions of anger are often so subtle that no one else notices. His imagination is both a strength and a source of anxiety; he frequently imagines frightening and worst-case scenarios for unfamiliar situations, with a particular recurring fear of a cave-dwelling monster known as the Cave Man.

Bonobono's primary motivation is simple: to understand the world and enjoy his daily life with his friends. He is often seen pondering philosophical or mundane questions, and his gentle quest for answers forms the core of his interactions. In the story, he serves as the central figure around whom the other characters revolve. His innocent perspective and questions often act as a catalyst for the events of each episode, prompting his friends to react, explain, or join him in his explorations.

His key relationships are with his two best friends, a chipmunk named Porori and a raccoon named Neoburi. Porori is often cynical and frequently tormented by his sisters, while Neoburi has a short temper and tends to bully Porori, creating a classic comedic trio dynamic. Bonobono shares a close and loving bond with his father, a somewhat bumbling but caring figure who also speaks with a slow, halting cadence. He also looks up to the Fishing Cat, a strong and sensible outsider who is considered the strongest animal in the forest and often serves as a source of wisdom for the young otter.

Throughout the series, Bonobono shows a subtle but noticeable development. In his earliest appearances, he almost never got angry. Over time, he becomes more expressive, to the point where it becomes normal for him to shout and react strongly to the antics of those around him, a significant shift from his original, more passive character. Physically, his design also evolved, moving from a chubby, rounded appearance to a noticeably slimmer figure as the art style progressed.

Bonobono has several notable abilities and habits. He is almost never seen without a clam or shellfish, which he carries as an emergency food source, often holding one in his hand or storing a spare in his armpit, a habit reflecting real sea otter behavior. He uses the shell to make tapping sounds, sometimes to communicate or express himself. As a marine animal, he is a strong swimmer and can dive, though he is notably slower and clumsier when moving on land. Despite his generally docile nature, he possesses surprising physical strength, which became evident on a rare occasion when he ate a poisonous mushroom and became violent, or when he single-handedly held onto a rope to prevent an accident.