High fill structures are widely constructed to accommodate the connection between wharfs and landside areas in port engineering. The fill structures face a challenge from the water level fluctuation in port areas. In this study, based on a fill structure prototype under construction, a physical model test and a series of numerical analyses were conducted to study the deformation and stability of high fill structures in port areas under periodic water level fluctuations. The stress, displacement, and stability responses of the fill model to the water level fluctuation were investigated. The influences of the soil-rock ratio on deformation and the water level fluctuation on displacement and stability were further discussed. The results show that the displacement of the fill structure is affected by the soil-rock ratio of the fill material, and the decrease of the soil-rock ratio can improve the soil strength and thereby limit the fill deformation. As the water level draws down and the number of the fluctuation in water level increases, the fill displacement increases. The water level fluctuation has a significant influence on the fill stability. The stability increases slightly with the rise of the water level whereas it decreases significantly with the rapid fall of the water level. Therefore, adequate engineering interventions may be taken to prevent the fill instability. This study provides a reference for the design and construction of inland port projects.