Iori Kitahara is a young man with a dream. As he arrives in the scenic Izu Peninsula to begin his freshman year of college, he envisions the quintessential campus experience filled with new friends and romantic encounters. He plans to stay above his uncle's scuba diving shop, Grand Blue, a place he assumes will be a quiet and convenient base for his new life. This assumption is shattered the moment he opens the door, finding himself face-to-face with a room full of muscular, completely naked upperclassmen engaged in a raucous drinking party.

Before Iori can escape, he is forcefully recruited by the senior members, Shinji Tokita and Ryuujirou Kotobuki, into the university's diving club, Peek a Boo. However, the club's activities have little to do with the ocean. Instead, its members dedicate their free time to elaborate drinking binges, stripping down to their underwear or less, and engaging in absurd, shirtless competitions. Iori is immediately swept into this chaotic world of wild parties, peer pressure, and humiliation, much to the disgust of his cousin and new classmate, Chisa Kotegawa, who finds him in a compromising state. The initial narrative arc establishes this core conflict: Iori's desperate attempts to fit in and pursue his dream college life are constantly derailed by the club's hedonistic antics, which he is powerless to resist.

The cast of characters is central to the series' humor. Iori soon finds a reluctant partner-in-crime in Kohei Imamura, an otaku classmate who dreams of a harem of anime girls but is just as easily corrupted and dragged into the club's debauchery. The two become a comedic duo, their reactions to the escalating madness around them serving as a primary source of comedy. The senior club members, the ever-drinking Tokita and the stoic but equally naked bartender Kotobuki, are the chaotic catalysts who treat Iori and Kohei like their personal playthings. Providing a contrast are the female members: the sensible and athletic Chisa, who is genuinely passionate about diving and often serves as the embarrassed straight-woman to the boys' antics; her older sister Nanaka, a kind and voluptuous diving instructor with a hidden infatuation for Chisa; and the mischievous Azusa Hamaoka, a senior who is just as comfortable joining the drinking parties as the men.

As the series progresses, the narrative expands beyond the dive shop. A notable early arc involves the boys accidentally making enemies of the tennis club, leading to a hilarious and high-stakes showdown that parodies sports anime tropes. Another significant arc introduces Aina Yoshiwara, a freshman from a women's college who initially appears as a rival from the tennis club but eventually becomes a core member of Peek a Boo. Initially hiding behind heavy makeup and a fake persona, Aina finds acceptance and friendship within the diving club, learning to embrace her true self, and develops a romantic interest in Iori. The series also features a trip to Okinawa, which the characters treat as a sacred mission to experience an ancient drinking ritual, and a university festival arc where the club's attempts to run a simple café spiral into predictable chaos.

Despite the relentless focus on alcohol-fueled humor and male nudity, the series consistently circles back to its titular theme. Interspersed between the parties are surprisingly genuine and well-depicted scuba diving sequences. Chisa, Nanaka, and other members take the sport seriously, and the anime takes time to accurately portray the equipment, safety protocols, and the serene beauty of the underwater world. For Iori, who cannot even swim at the start, learning to dive becomes a genuine personal goal and a way to connect with his cousins on their own terms. These moments of earnest passion for the ocean provide a beautiful and calming counterbalance to the on-land chaos, ultimately revealing that beneath the wild exterior, the members of Peek a Boo share a deep bond of friendship and a true love for the Grand Blue sea.