Adaptive equalization algorithms efficiency in hydroacoustic communication systems with FBMC modulation is being investigated. In particular, estimation algorithms based on blind equalization methods, conventional LMS and RLS algorithms using pilot signals, which is combined with linear and decision feedback equalization techniques, are being considered. In addition, the MMSE equalizer with channel estimation using pilots is analyzed for comparison. The equalizers are applied to the QAM-FBMC system with Hermite filter prototypes. The simulation is performed using open source software for Filter Bank Multicarrier Modulation. The channel was being simulated using Brest Commercial Harbor experimental data from Watermark benchmark.The investigation shows that the considered adaptive equalizers with several taps are applicable only for small number of subcarriers (10 subcarriers considered). For large number of subcarriers (250 subcarriers considered) the one-tap equalizers with per-frame estimation show better results, because of subchannel frequency response flatness and channel nonstationarity. Among the equalizers considered, the better results for 250 subcarriers are achieved for the MMSE with 12.5% of pilots in overall signal, suitable results were also obtained for linear RLS equalizer with one-tap estimator. For 10 subcarriers best result is achieved for LE-RLS algorithm with 2–4 taps.