With the growing application of micro aerial vehicles (MAVs), novel configurations—such as flying-wing waterborne MAVs equipped with vectored thrust—are emerging, combining the aerodynamic efficiency of fixed-wing designs with the versatility of water take-off and landing. These air–water multi-modal platforms broaden operational capabilities to include missions over rivers, ponds, and lakes, particularly in environments lacking conventional runways. However, water landings present unique challenges, including the need to minimize touchdown velocity, maintain stable pitch attitude, and mitigate impact loads to protect structural integrity. To address these challenges, this work proposed a non-linear model predictive control (NMPC) based trajectory planning framework that jointly optimizes altitude and pitch angle tracking over a specified prediction horizon. By integrating coordinated inner-loop attitude stabilization with outer-loop trajectory shaping, the system produces smooth, energy-efficient descent profiles that ensure safe water touchdowns. Simulation results demonstrate that the proposed approach effectively balances descent rate, energy consumption, and stability, offering a reliable and robust guidance solution for waterborne MAV operations.