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. The study was carried out between October, 2007 and October, 2008. Physical and chemical parameters (temperature, pH, dissolved oxygen, salinity, turbidity, hardness, alkalinity, ammonia nitrogen, nitrite, nitrate, phosphate, silica) and biological parameters (chlorophyll-a, fecal coliforms, Vibrio and bacteria counts) were analyzed. To assess the dependency relationship between the variables the non-parametric correlation test of Spearman was applied. The Hydrological Index (HI) c was applied to evaluate the potential use of the two coastal areas for shrimp culture. The Canadian Water Quality Index (CCME WQI) was applied to compare the water quality parameters between the shrimp farm water supply lagoon and those two coastal environments. Results indicate water quality parameters and times of the year are related to environmental stress. Considering the amplitude of the variables monitored, i.e., temperature, salinity, pH, alkalinity, hardness, nitrate and silica, autumn may be associated with increased environmental stress. The (HI) c indicated that pumping water into the shrimp farm in spring and summer should be restricted, and during the rest of the year the supply water quality ranged from “suitable with medium restriction” (5.5 < (IH) c < 7.5) to “suitable with low restriction” (7.5 < (IH) c < 9.0). No difference was detected in the water quality parameters of the three study sites according to the CCME WQI. The application of a Water Quality Index adapted to the different production activities is useful to monitor water quality parameters. The WQI is practical, with easy and fast interpretation of data, and an important management tool for aquaculture enterprises.