"Squid Girl" centers around a young, anthropomorphic squid who emerges from the ocean with the intent to conquer humanity as retribution for polluting the seas. Calling herself "Invader from the Sea," she quickly discovers her plans are far more challenging than anticipated. Her first encounter with humanity occurs at a beachside restaurant called the Lemon Beach House, where she accidentally damages the property. To repay the debt, she begins working at the restaurant alongside the Aizawa siblings, Chizuru and Eiko, who manage the establishment.

The series unfolds as a slice-of-life comedy, with Squid Girl's attempts to adapt to human society often leading to humorous misunderstandings and mishaps. Her unique abilities, such as extending her tentacle-like hair and emitting ink, frequently cause chaos, but her earnest and naive personality endears her to those around her. Over time, her initial goal of world domination fades as she becomes more integrated into human life, forming bonds with the Aizawa siblings, their friends, and other quirky characters.

Key characters include Chizuru Aizawa, the stern but caring older sister who often keeps Squid Girl in check; Eiko Aizawa, the more laid-back and supportive younger sister; and Takeru, a young boy who idolizes Squid Girl and frequently joins her adventures. Other recurring characters, such as the competitive diver Goro and the mysterious scientist Nagisa, add variety to the interactions and comedic scenarios.

The narrative structure is episodic, with each episode featuring self-contained stories that highlight Squid Girl's growth and her evolving relationships with the human world. Themes of environmental awareness are subtly woven into the humor, as Squid Girl's initial motivation stems from humanity's mistreatment of the ocean. However, the focus remains on lighthearted comedy and the charming dynamics between the characters. The series balances absurdity with heartfelt moments, creating a whimsical yet relatable portrayal of an outsider finding her place in an unfamiliar world.