This paper presents a novel model for assessing the water quality for the artificial habitat in shrimp aquaculture. The physical-chemical variables involved in the artificial habitat are measured and studied for modeling the environment of the ecosystem. A new physical-chemical index (Г) classifies the behavior of the environmental variables, calculating the frequency and the deviations of the measurements based on impact levels. A fuzzy inference system (FIS) is used for establishing a relationship between environmental variables, describing the negative ecological impact of the concentrations reported. The FIS uses a reasoning process for classifying the environmental levels providing a new index, which describes the general status of the water quality (WQI); excellent, good, regular and poor.