Nowadays, numerical flow and water quality models are widely applied to solve coastal engineering problems. The outcomes of the algorithmic execution often deviate from those anticipated, particularly when the model is set up initially. This necessitates the modeler to perform the manipulation procedure, which comprises feed back and modification. As such, it is desirable that expert system technology be integrated into the modeling system to furnish assistance for the novice user who lacks the requisite knowledge to establish the model and assess the results. In this paper, a prototype expert system on manipulation of numerical coastal flow and water quality models is developed and implemented by employing an expert system shell, Visual Rule Studio, as an Active Designer under Microsoft Visual Basic environment. Through the successful development of this prototype system, it is shown that the expert system technology can be coupled into numerical modeling for mimicking the manipulation process. It assists the user to formulate a suitable strategy for striking a balance between accuracy and effectiveness and to tune the model to accomplish satisfactory modeling of real phenomena. It is able to bridge the existing gap between numerical modelers and practitioners in this field.