We study the dynamics of a dipolar Bose-Einstein condensate, like for example a 52 Cr or 164 Dy condensate, interacting with a superconducting surface. The magnetic dipole moments of the atoms in the Bose-Einstein condensate induce eddy currents in the superconductor. The magnetic field generated by eddy currents modifies the trapping potential such that the center-of-mass oscillation frequency is shifted. We numerically solve the Gross-Pitaevskii equation for this system and compare the results with analytical approximations. We present an approximation that gives excellent agreement with the numerical results. The eddy currents give rise to anharmonic terms, which leads to the excitation of shape fluctuations of the condensate. We discuss how the strength of the excitation of such modes can be increased by exploiting resonances, and we examine the strength of the resonances as a function of the center-of-mass oscillation amplitude of the condensate. Finally, we study different orientations of the magnetic dipoles and discuss favorable conditions for the experimental observation of the eddy current effect.