The semi-enclosed estuary is very susceptible to changes in the physical and environmental characteristics of the inflow from the land and the coastal sea weather and so the continuous and comprehensive monitoring is necessary for managing the estuary. Nevertheless, the standard procedure or schematic framework has not been proposed appropriately to determine how many instruments are necessary and where they need to be deployed to detect critical changes. Therefore, the present work proposes a systematical strategy for the deployments of the monitoring array by using the combination of the graphical optimization with the objective mapping technique. In order to reflect the spatiotemporal characteristics of the bay, the representative variables and eigenvectors are determined by the Empirical Orthogonal Function (EOF), and the cosine angle among them are calculated for a design index of optimization. At the recommended locations, the sampled representative variables are interpolated to reconstruct their spatiotemporal distribution and compared with the distributions of the true values. Analysis confirms that the selected locations, even with a small number of points, can be used for on-site monitoring. Also, the present framework suggests how to determine installable regions for real-time monitoring stations, which reflect the global and local characteristics of the semi-enclosed estuary.