This paper presents a one-dimensional time-dependent numerical model of a sea organ, which generates music driven by the motion of the sea. The governing equations are derived by coupling hydrodynamic and thermodynamic equations for water level and air pressure oscillations in a sea organ pipe system forced by irregular waves. The model was validated by comparing numerical results to experimental data obtained from a scaled physical model. Furthermore, the model’s capabilities are presented by simulating internal oscillations in the Sea Organ in Zadar, Croatia. The response of the Sea Organ varies between segments and for different wave conditions. The strongest air pressure and water level response is found near resonance frequencies.