H₂O's story revolves around Takuma Hirose, a blind young male junior-high school student, though the cause for his blindness is undetermined. After his mother died an unexpected death, it left a deep emotional scar on him, which caused him to become very lonely and reserved. Due to this, Takuma and his uncle move from the city out into a rural area and Takuma is enrolled into a new junior-high school. At his new school, he meets several new girls, though three of whom he gets to know the most out of anyone else. They are, the firm and obstinate Hayami Kohinata, the kind and obliging Hinata Kagura, and the cheerful and mysterious Otoha. As Takuma interacts with these girls, his medical condition gradually begins to heal.