The backscattering effects degrade the detection performance in a full-duplex underwater optical wireless communication (UOWC) system when the power of received backscattering interference is comparable to that of a target signal. In this paper, the orthogonal waveforms with the Hermite–Gaussian function and prolate spheroidal wave function are first introduced for a pulse position modulation based dynamic UOWC system to alleviate the backscattering effects. Then, a joint maximum likelihood detection scheme is proposed accordingly. Experimental results verify the superiority of the proposed method with orthogonal waveforms over the scheme without orthogonal pulse shaping in a dynamic underwater bubbly channel.