Polarization and phase modulation noises caused by the lead fiber are harmful to a long-haul fiber hydrophone system. In this paper we used a pressure and acceleration insensitive reference hydrophone to obtain the lead fiber induced common noise, and then used adaptive noise cancellation to remove them from a primary hydrophone. Experimental results show that by the use of Normalized Least-mean-square (NLMS) algorithm, a broadband polarization noise caused by disturbing the lead fiber is suppressed by maximal 20 dB and a narrowband phase modulation noise is suppressed by 20 dB. Thus the lead fiber induced noise is eliminated and no reduction in the amplitude of the simulated signal is found. It is shown that the results of adaptive noise cancellation are much better than that of the noise subtract method.