This article shows that the added mass due to fluid-structure interaction significantly affects the vibrational dynamics of cilia-based (vibrating cantilever-type) devices for handling microscale fluid flows. Commonly, the hydrodynamic interaction between the cilia-based actuators and fluid is modeled as a drag force that results in damping of the cilia motion. Our main contribution is to show that such damping effects cannot explain the substantial reduction in the resonant-vibrational frequency of the cilia actuator operating in liquid when compared with the natural frequency of the cilia in air. It is shown that an added-mass approach (that accounts for the inertial loading of the fluid) can explain this reduction in the resonant-vibrational frequency when operating cantilever-type devices in liquids. Additionally, it is shown that the added-mass effect can explain why the cilia-vibration amplitude is not substantially reduced in a liquid by the hydrodynamic drag force. Thus, this article shows the need to model the added-mass effect, both theoretically and by using experimental results.