Filtered multitone (FMT) modulation divides the communication band into several subbands to shorten the span of symbols affected by multipath in underwater acoustic (UWA) communications. However, there is still intersymbol interference (ISI) in each subband of FMT modulation degrading communication performance. Therefore, ISI suppression techniques must be applied to FMT modulation UWA communications. The suppression performance of traditional adaptive equalization methods often exploited in FMT modulation UWA communications is limited when the effect of ISI spans tens of symbols or large constellation sizes are used. Turbo equalization consisting of adaptive equalization and channel decoding can improve equalization performance through information exchanging and iterative processes. To overcome the shortcoming of traditional minimum mean square error (MMSE) equalization and effectively suppress the ISI with relatively low computation complexity, an FMT modulation UWA communication using low-complexity channel-estimation-based (CE-based) MMSE turbo equalization is proposed in this paper. In the proposed method, turbo equalization is first exploited to suppress the ISI in FMT modulation UWA communications, and the equalizer coefficients of turbo equalization are adjusted using the low-complexity CE-based MMSE algorithm. The proposed method is analyzed in theory and verified by simulation analysis and real data collected in the experiment carried out in a pool with multipath propagation. The results demonstrate that the proposed method can achieve better communication performance with a higher bit rate than the FMT modulation UWA communication using traditional MMSE adaptive equalization.