Atmospheric pressure plasma-liquid interactions exist in a variety of applications, including wastewater treatment, wound sterilization, and disinfection. In practice, the phenomenon of liquid surface depression will inevitably appear. The applied gas will cause a depression on the liquid surface, which will undoubtedly affect the plasma generation and further affect the application performance. However, the effect of liquid surface deformation on the plasma is still unclear. In this work, numerical models are developed to reveal the mechanism of liquid surface depressions affecting plasma discharge characteristics and the consequential distribution of plasma species, and further study the influence of liquid surface depressions of different sizes generated by different helium flow rates on the plasma. Results show that the liquid surface deformation changes the initial spatial electric field, resulting in the rearrangement of electrons on the liquid surface. The charges deposited on the liquid surface further increase the degree of distortion of the electric field. Moreover, the electric field and electron distribution affected by the liquid surface depression significantly influence the generation and distribution of active species, which determines the practical effectiveness of the relevant applications. This work explores the phenomenon of liquid surface depression, which has been neglected in previous related work, and contributes to further understanding of plasma-liquid interactions, providing better theoretical guidance for related applications and technologies.