Two modifications for solar desalination systems are presented. The first modification, using a packed layer that installed in the bottom of the basin to increase the efficiency of the still. A packed layer is formed from glass balls which is considered as simple thermal storage system. The second modification, using rotating shaft installed close to the basin water surface. The target of using the rotating shaft to break the boundary layer of the basin water surface, thus increasing the water vaporization and condensation, the performance of the present solar desalination system may also be increased. The numerical analysis presented the equations of the direct coupling of the selected PV-solar panel, DC-motor and inverter for small PV-system. The characteristics of PV array and the DC-motor are presented for the specific PV–DC power. The performance of the two modified solar stills and the conventional one is compared. Three experiments were carried out using the climate conditions of Cairo site, Egypt. Transient temperatures of the two modified solar stills and the conventional one are measured from sunrise to sunset with the same operating parameters. The energy equations that governed the present solar desalination system are presented. Energy absorbed by glass cover, basin water, packed layer and the required power of the rotating shaft are calculated to obtain the water productivity and efficiency of the present systems. The results show that the two modifications enhanced the performance of the solar desalination system. The efficiency of the modified solar desalination system using packed layer thermal energy storage was increased by 5% at May, 6% at June, and 7.5% at July, while it was increased by 2.5% at May, 5% at June, and 5.5% at July for the modified one using rotating shaft and PV-system.