In this study, a hybrid solar desalination system incorporating thermoelectric modules and a Vertical Multi-Effect Distillation (VMED) unit was experimentally investigated. The primary objective is to enhance the efficiency of brackish water desalination by integrating solar energy technologies, waste heat recovery, and multi-stage distillation. The system utilizes photovoltaic-thermal (PV/T) panels to simultaneously supply electrical and thermal energy, while thermoelectric modules are employed to recover lost heat and improve overall system performance. The VMED mechanism leverages the heat provided by the PV/T panels to achieve high-efficiency distillation. The effects of parameters such as solar radiation intensity, temperature gradient across the thermoelectric modules, and water column height on system performance were examined. Results demonstrate that integrating thermoelectric technology with the VMED process increases the overall system efficiency by up to 23% compared to conventional methods, achieving a freshwater production rate of 36 liters per day. The performance of the hybrid system with thermoelectric modules highlights the positive impact of enhanced heat transfer on evaporation and condensation processes. Increasing the number of vertical distillation stages to five yielded optimal performance. Moreover, statistical analyses revealed that the deviation between the proposed correlation and experimental data ranged from −5% to +10%, with a mean absolute deviation of 3.24%. A correlation coefficient (R²) of 0.96 confirms the excellent agreement between the proposed model and experimental results. This study offers a sustainable and efficient solution for freshwater supply in arid and water-scarce regions.