SummaryDeveloping a reliable and robust underwater acoustic communication system is a difficult task due to the complicated nature of the underwater channel, non‐stationary noise, and several other factors. Indeed, channel estimation or equalization presents numerous challenges in this non‐stationary, highly Doppler, multipath environment; as a result, traditional equalizers and PLL‐based methods have limited performance. Generally, communication over such time‐varying channels is accomplished via packets that contain a prefix/preamble signal for training, a payload containing the actual data, and a silent period for proper alignment. The prefix signal must be designed properly because it is used to estimate the channel and determine the start of the packet. In this paper, we propose a new prefix signal based on the hyperbolic chirp signal, which has Doppler invariance properties. These properties enable the extraction of the entire packet even under severe multipath and Doppler. Our new proposed prefix signal can accurately and efficiently characterize an underwater channel by estimating the multipath delay, amplitude, and Doppler scales. Our new method has been validated through extensive simulations using various channel models for its robustness and effectiveness under various conditions. It has also been tested on a real‐world channel.