—In this paper, we propose to use cross recurrence plot analysis (CRPA) to estimate the time-difference of arrival (TDOA) of underwater acoustic signals arriving on an array of hydrophones. Instead of considering the signal as a whole to estimate the TDOA, like classical methods do, we first detected the series of samples that look alike on each pair of hydrophones of the array by using cross-recurrence plot analysis. The TDOA is then estimated by relying only on these common sample series. The TDOA estimator is based on quantification measures specifically designed for CRPA. The proposed method is successfully validated on real data containing frequency-modulated sounds from beluga whales.