The continuous monitoring of physical, chemical and biological parameters in shrimp culture is an important activity for detecting potential crisis that can be harmful for the organisms. Water quality can be assessed through toxicological tests evaluated directly from water quality parameters involved in the ecosystem; these tests provide an indicator about the water quality. The aim of this study is to develop a fuzzy inference system based on a reasoning process, which involves aquaculture criteria established by official organizations and researchers for assessing water quality by analyzing the main factors that affect a shrimp ecosystem. We propose to organize the water quality parameters in groups according to their importance; these groups are defined as daily, weekly and by request monitoring. Additionally, we introduce an analytic hierarchy process to define priorities for more critical water quality parameters and groups. The proposed system analyzes the most important parameters in shrimp culture, detects potential negative situations and provides a new water quality index (WQI), which describes the general status of the water quality as excellent, good, regular and poor. The Canadian water quality and other well-known hydrological indices are used to compare the water quality parameters of the shrimp water farm. Results show that WQI index has a better performance than other indices giving a more accurate assessment because the proposed fuzzy inference system integrates all environmental behaviors giving as result a complete score. This fuzzy inference system emerges as an appropriated tool for assessing site performance, providing assistance to improve production through contingency actions in polluted ponds.