In this study new extensions of the theoretical models developed by Molin (2001) and Molin et al. (2018) are proposed to solve the resonance problem for three-dimensional circular and rectangular moonpools with recesses. Eigenfunction expansions are adopted to describe the velocity potentials in all the subdomains. Then, the velocity potentials and normal velocities are matched at the common boundaries such that the eigenvalue problems are formulated and solved, yielding the natural frequencies and associated modal shapes of the free surface. Both the models for infinite and finite water depths are derived for circular moonpools with recesses. Applications are also made for the three-dimensional rectangular moonpools with recesses. In addition, frozen-mode approximation is derived, which yields simple formulas for prediction of the natural frequencies for piston-mode resonances. The proposed models in this study are validated by comparing the obtained results with the experimental data and the results using other numerical models. Moreover, for the first sloshing mode in rectangular moonpool, simple approximation model is proposed based on the assumption that the half of the wavelength of a standing wave is the same as the moonpool length. The validity of the model is examined by comparing the solutions with the results by the diffraction–radiation code WAMIT.