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In this paper, we propose a dynamic displacement estimation method for large-scale civil infrastructures based on a two-stage Kalman filter and modified heuristic drift reduction method. When measuring displacement at large-scale infrastructures, a non-contact displacement sensor is placed on a limited number of spots such as foundations of the structures, and the sensor must have a very long measurement distance (typically longer than 100 m). RTK-GNSS, therefore, has been widely used in displacement measurement on civil infrastructures. However, RTK-GNSS has a low sampling frequency of 10–20 Hz and often suffers from its low stability due to the number of satellites and the surrounding environment. The proposed method combines data from an RTK-GNSS receiver and an accelerometer to estimate the dynamic displacement of the structure with higher precision and accuracy than those of RTK-GNSS and 100 Hz sampling frequency. In the proposed method, a heuristic drift reduction method estimates displacement with better accuracy employing a low-pass-filtered acceleration measurement by an accelerometer and a displacement measurement by an RTK-GNSS receiver. Then, the displacement estimated by the heuristic drift reduction method, the velocity measured by a single GNSS receiver, and the acceleration measured by the accelerometer are combined in a two-stage Kalman filter to estimate the dynamic displacement. The effectiveness of the proposed dynamic displacement estimation method was validated through three field application tests at Yeongjong Grand Bridge in Korea, San Francisco–Oakland Bay Bridge in California, and Qingfeng Bridge in China. In the field tests, the root-mean-square error of RTK-GNSS displacement measurement reduces by 55–78 percent after applying the proposed method. Full article