Inland lakes or reservoirs are the main surface water resources, related to people’s survival and social development. On-site water level data are critical for water resource management, while satellite laser and remote sensing data are a significant tool for long-term change monitoring. In this study, we took the Miyun Reservoir, the most important source of drinking water in Beijing, as the research area. We used Landsat images and the Ice, Cloud, and Land Elevation Satellite (ICESat-2) for small-scale water level change monitoring and inversion across unrecorded periods. First, we proposed a new two-step denoising method based on local statistics to denoise the ATL03 single photon data from 2018 to 2020, and extracted the effective elevation information of Miyun Reservoir. Second, based on Landsat images from 1984 to 2020, the MNDWI index was used to extract the water area and generated a percentage map of water occurrence. Finally, the water and land boundary elevation were selected from the effective photon elevation information according to the boundary position under each percentage of the water generation percentage graph, the area, and the water level elevation model (A–E model) was established, and the water level values of unrecorded periods were inverted. The denoising results showed that the denoising accuracy of all data is higher than 95%. The area of Miyun Reservoir has changed greatly in the past 37 years, especially in the northeast corner and northern region. The inverted water level elevation had a strong correlation with the measured value, the correlation coefficient reached 0.97, the root mean square error (RMSE) was 0.553 m, and the estimated water level value was highly consistent with the recorded value and fluctuated dramatically from 1984 to 2020. This method complements the traditional water level mapping method, provides a new idea for the monitoring of water level changes in lakes or reservoirs without field records, and also contributes to the timely and effective monitoring and management of global lake and reservoir water level and time changes.