This study illustrate the use of indicators and models to support the Ecosystem Approach to Fisheries and Aquaculture management using two case studies in Chile: prediction of environmental variability effects upon anchovy (Engraulis ringens) fishery of northern Chile and prediction of suitable sites and carrying capacity of Pacific oyster (Crassostrea gigas) culture using FARM and geographic information system (GIS) models in the Valdivia estuary. A three stage approach was applied: Stage 1 considers spatiotemporal ecosystem indicators (fisheries, aquaculture, environmental, and regulatory), Stage 2 uses statistical relationships between indicators, GIS, and other simulation models (e.g., artificial neural networks and FARM) of environment-resources interaction, and Stage 3 is the analysis and validation of models outputs. The methodology illustrates how indicators and models may be used to assist decision-makers in developing an ecosystem approach to fisheries and aquaculture. The application of these approaches provides an integrative methodology for abundance prediction of anchovy and site selection for shellfish aquaculture, despite limitations in the available data.