Controlling the hydraulic heads along a coastal aquifer may help to effectively manage saltwater intrusion, improve the conventional barrier’s countermeasure, and ensure the coastal aquifer’s long-term viability. This study proposed a framework that utilizes a decision-making model (DMM) by incorporating the results of two other models (physical and numerical) to determine proper countermeasure components. The physical model is developed to analyze the behavior of saltwater intrusion in unconfined coastal aquifers by conducting two experiments: one for the base case, and one for the traditional vertical barrier. MODFLOW is used to create a numerical model for the same aquifer, and experimental data are used to calibrate and validate it. Three countermeasure combinations, including vertical barrier, surface, and subsurface recharges, are numerically investigated using three model case categories. Category (a) model cases investigate the hydraulic head’s variation along the aquifer to determine the best recharge location. Under categories (b) and (c), the effects of surface and subsurface recharges are studied separately or in conjunction with a vertical barrier. As a pre-set of the DMM, evaluation and classification ratios are created from the physical and numerical models, respectively. The evaluation ratios are used to characterize the model case results, while the classification ratios are used to classify each model case as best or worst. An analytical hierarchy process (AHP) as a DMM is built using the hydraulic head, salt line, repulsion, wedge area, and recharge as selection criteria to select the overall best model case. According to the results, the optimum recharging location is in the length ratio (LR) from 0.45 to 0.55. Furthermore, the DMM supports case3b (vertical barrier + surface recharge) as the best model case to use, with a support percentage of 48%, implying that this case has a good numerical model classification with a maximum repulsion ratio (Rr) of 29.4%, and an acceptable wedge area ratio (WAR) of 1.25. The proposed framework could be used in various case studies under different conditions to assist decision-makers in evaluating and controlling saltwater intrusion in coastal aquifers.