The continuous monitoring of the physical, chemical and biological parameters of pond, effluent and inlet waters helps not only to predict and control negative conditions for shrimp farming, but also avoids environmental damages and collapse of the production process. The objective of this study was to demonstrate the importance of implementing a Water Quality Index (WQI) as a tool to manage shrimp farms and the surrounding natural environments, further to understand the main factors affecting water quality to prevent disease outbreaks. Water quality parameters of shrimp pond and inlet waters were monitored and measured monthly in a shrimp farm and in two other natural sites in northern Santa Catarina state, Brazil.