Ecological modeling has been used as a tool to estimate potential impacts caused by aquaculture to the surrounding environment. In this work, a mathematical model was applied to estimate the maximum amount of pink shrimp (Farfantepenaeus paulensis) culture units (3,100m2 pen enclosures) that could be installed at two shallow estuarine bays of Patos Lagoon (known as Coreia and Porto do Rei) with no significant effects on either water quality or viability of the culture system. To calibrate the model, information about the culture of Litopenaeus vannamei and F. paulensis as well as field data (influence of netting material, water current speed and nitrogen concentrations) were used. Under a bad scenario (water current velocity of 0.01m s-1 and a mesh clogging effect of 40%), it would be possible to install up to 29 pens at the Coreia bay, and 39 pens at the Porto do Rei bay. Results indicate that the model was useful in determining the maximum number of culture units that could be installed at these bays, and thus have the potential to become an important tool in the definition of environmental management strategies in relation to aquaculture development.