Water literacy has become a fundamental aspect in today’s society, as its conservation, preservation and management is key to ensuring human survival. The purpose of this paper was to analyze the effectiveness of flipped learning methodology on a traditional training practice in water literacy at the first level of secondary education. The flipped learning method consisted in providing the contents to the students before the class sessions, encouraging an active learning. A descriptive study was adopted with two experimental groups, two control groups and only post-test. An ad hoc questionnaire was used as an instrument to measure the parameters: Socio-educational, Motivation, Interactions, Autonomy, Collaboration; Deepening of contents; Problem solving, Class time and Ratings. The final sample was composed of 120 students, divided into four groups of 30 students each. The application of the treatment in the experimental groups lasted 10 sessions of 55 min. The results indicate that the use of time in class, the autonomy and the deepening of the contents were the aspects that improved most with the flipped learning approach. However, no significant differences in ratings were found. Finally, the main findings and their implications for water literacy are discussed.