Faster-Than-Nyquist (FTN) signaling is a promising technique to enhance the UnderWater Acoustic (UWA) communications rate. However, the main issue of this technique is Inter-Symbol Interference (ISI) that needs to be tackled efficiently at the receiver side. To face this issue, we propose a new Hybrid Time-Frequency Domain Equalizer (HTDFE) for FTN UWA communication systems. In contrast to the conventional HTDFE, each Frequency Domain Equalizer (FDE) at the multiple output side is followed by a joint phase estimator and feedforwardfeedback Time Domain Equalizer (TDE). Simulations over a real underwater channel show that the proposed algorithm allows a gain in performance compared to the conventional solutions.