This study presents the design of a high-efficiency pulse width modulation (PWM) power amplifier for marine biological sound reproduction. Due to the capacitive nature of underwater transducers and step-up transformers, output LC filter design is constrained, making it difficult to achieve a flat frequency response and low total harmonic distortion (THD). To address this, the electrical characteristics of these components were measured and modeled to construct equivalent circuits for the PSPICE simulator. Based on these models, an optimized LC filter was designed, and its performance was validated through simulation and experiments. The cause of THD occurring in specific frequency bands was analyzed, and two types of notch filters were applied to improve THD and switching signal attenuation. The proposed methodology offers a practical approach to improving PWM amplifier performance in underwater acoustic systems, supporting the development of compact, efficient, and reliable SONAR transmitters.