In the context of the design of a simple lightweight underwater positioning system aboard a boat, we aim to develop an innovative approach for path difference estimation. In this work, we consider a spread spectrum communication system with a CDMA-BPSK modulation. Communications are realized between a transceiver, an underwater transponder and two hydrophones. The two hydrophone signals are integrated before sampling. In order to estimate the path delay, we perform a correlation of the received signal with a locally generated replica. The main feature of our technique is that the local replica is a BOC (Binary Offset Carrier) modulated code. The resulting cross-correlation function has a specific form with a sequence of multiple sub-peaks. Based on this form, we implement a processing algorithm that is able to distinguish overlapping correlation peaks on the signals sum. Simulation and experimental tests have been carried out to approve this delay estimating method and evaluate its performances.