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The authors have been developing an acoustic observation system that can record the high frequency bio-sonar clicks of the Ganges river dolphins and can estimate their 3-D location in real-time. In order to expand the coverage of the acoustic measurement, a new integrated observation system, which consists of one main array system and the newly developed multiple small array system, is proposed. For the first step, we deployed one main array and one small 4-hydrophone cross array system in the Ganges River. Combining the measurement results of the two array systems, we successfully obtained improved estimates of acoustic positions of the sound source than that of a single stand-alone measurement.