Water quality assessment is an important activity for controlling harmful crisis in aquaculture systems. The objective of our study was to develop a new Water Quality Index focused on monitoring of shrimp farms; detecting poor water quality and preventing negative effects in the ecosystem. Usually, several water quality parameters are monitored and measured in a shrimp farm during a farming period. Those parameters are classified according to their negative effects in the ecosystem and their respective allowed limits are also defined. The proposed Water Quality Index assigns a priority level to each water parameter through a new analytical hierarchical process (AHP), which allows an accurate assessment of the water quality. Our proposed index was applied to assess the water quality condition in extensive shrimp farms in Mexico. A comparison between our approach and those proposed in the literature shows its good performance when real environments are assessed.