The underwater (UW) acoustic channel poses multiple challenges like coloured ambient noise, frequency‐dependent attenuation, and doubly selective fading. The availability of a robust underwater communication mechanism can largely enhance the success of human effort in a multitude of applications, ranging from pollution surveillance to defence and search/rescue operations. In this work, generalized frequency division multiplexing (GFDM), a non‐orthogonal multicarrier scheme, which has recently been studied for terrestrial wireless fading channels, is developed and tested for signalling in UW acoustic communication. UW noise, attenuation, and doubly selective fading channels are modelled with appropriate statistics. The BER performance of proposed system is systematically evaluated under different channel conditions, starting from simple additive white Gaussian noise (AWGN) and Rayleigh fading channels to a horizontally configured UW channel. The performance is also compared with contemporary orthogonal frequency‐division multiplexing (OFDM)– and filter bank multicarrier (FBMC)–based systems.