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It is essential to accurately estimate rainfall to predict and prevent hydrological disasters such as floods. In this paper, an electromagnetic wave rain gauge system and a method to estimate average rainfall using the system’s multiple elevation observation data are presented. The compact electromagnetic wave rain gauge is a small-sized radar that performs very short-range observations using K-band dual-polarization technology. The method to estimate average rainfall is based on the concept of an average observation derived from multiple elevation scans with very short range and dual-polarization information. The proposed method was evaluated by comparing it with ground instruments, including a pit-gauge, tipping-bucket rain gauges, and a Parsivel disdrometer. The evaluation results demonstrated that the new methodology worked fairly well for various rainfall events.