Excessive settlement may induce structural damage and water leakage in immersed tunnels, seriously threatening the tunnels’ safety. However, making accurate assessment of the settlement in immersed tunnels is difficult due to the incomplete knowledge of the geotechnical parameters and the inadequacy of the model itself. This paper proposes an effective method to accurately assess the settlement in immersed tunnels. An enhanced beam on elastic foundation model (E-BEFM) is developed for the settlement assessment, with the Bayesian adaptive direct search algorithm adopted to estimate unknown model parameters based on previous observations. The proposed method is applied to a field case of the Hong Kong–Zhuhai–Macao immersed tunnel. The original BEFM is used for comparison to highlight the better assessment performance of E-BEFM, particularly for joints’ differential settlement. Results show that the proposed method can provide accurate predictions of the total settlement, angular distortion (a representation of tubes’ relatively differential settlement), and joints’ differential settlement, which consequently supports the associated maintenance decision-making and potential risk prevention for immersed tunnels in service.