A new algorithm for a compact mobile four-hydrophone array “RAPID Array” that displays the dolphin's real-time direction data on a graphical user interface (GUI) was proposed to accurately estimate the number of Ganges river dolphins from acoustic data recorded during the census. By considering the trajectory changes in dolphins' click data depending on the time (t) and azimuth (θ) in the coordinate space (t: time, θ: azimuth) on the GUI, the concept of “clustering” using the dolphins' direction data was introduced for developing the new algorithm. The proposed method could be applied using two modes: the online mode for real-time analysis at the observation site and offline mode for detailed analysis. Performance of the both online and offline modes of the developed algorithm using data from census conducted in 2015 and 2016 was clearly demonstrated. Periodic census using the RAPID Array with the proposed method will help in the behavioral analysis of Ganges river dolphins in their habitat in the Ganges river system.