This work presents a methodology for modelling and simulating aquatic ecological systems and an associated methodology and software for creating Decision Support Systems (DSS) for this kind of environment. Both are based on object oriented programming (OOP) and, in the case of the DSS, on Autonomous Intelligent Agents. The modelling software (EcoDynamo) includes several object dynamic link libraries to simulate different physical and biogeochemical ecosystem processes. These libraries were designed to be possible their linkage with different model shells, for the sake of portability and usability. A high level communication language (ECOLANG) was developed to allow the communication between EcoDynamo and the agents. The DSS uses one methodology of discrete multicriteria, where given a users preference structure (elicited with the Analytic Hierarchy Process methodology - AHP), a priority ranking of the preprocessed scenarios is achieved. To validate the approach, EcoDynamo was used with the DSS to simulate different management scenarios in a coastal lagoon at the South of Portugal - Ria Formosa. The experiments performed showed that these tools may be widely used by people involved in the management of coastal areas to integrate environmental, economic and social issues in the decision process, without an in-depth knowledge of modelling methodologies.