A large number of estuarine systems provide favorable conditions for aquaculture, including high nutrient content, sheltered waters, and favorable water temperatures. In this context, the main objective of this work is to identify the most suitable areas within the Ria de Alvor for bivalve and fish aquaculture production considering present and future conditions in a climate change context. A suitability index was developed based on the results of an annual simulation with the Delft3D model and the thresholds and optimal values of development of each species were analyzed. Generally, results suggest that the most suitable areas for aquaculture were located along the axis of the lagoon’s main channel, although seasonal variability was presented depending on the species. During winter and autumn, bivalves (oysters and mussels) are more susceptible to environmental conditions than fish. Conversely, spring presents the most favorable environmental conditions for the production of all species considered. Future projections indicate a general decrease in aquaculture suitability, particularly during winter for both bivalve species and during summer for Mussels, mostly due to the predicted increase in water temperature.