Satellite radar altimetry has been widely utilized in hydrological research, particularly with the advent of Sentinel-3, a Synthetic Aperture Radar (SAR) altimeter operating globally and equipped with an innovative onboard tracking system referred to as the open-loop tracking command (OLTC). Utilizing a pseudo-DEM (Digital Elevation Model), controlled through the OLTC, holds significant promise for the reliable observation of inland water bodies. Nevertheless, the complex geographical conditions in high mountain and reservoir river basins pose challenges in defining an appropriate pseudo-DEM for hydrological targets, potentially leading to reduced performance of Sentinel-3. This study aims to comprehensively evaluate the performance of Sentinel-3 by selecting the Lancang and Nu River basins in southwest China as a case study. These two rivers have a similar natural environment, but cascade reservoirs distinguish the Lancang River basin. By analyzing waveform energy from echoes of virtual stations (VSs) in both river basins (27 VSs in the Lancang River basin and 39 VSs in the Nu River basin), the performance of Sentinel-3 in different tracking modes and OLTC versions were compared. The results indicated that the detection rate of Sentinel-3A increased when transitioning from the closed-loop mode to the open-loop mode and with the implementation of newer OLTC versions (36.8% increased to 47.4%, 60.5%, and 63.2% in OLTC V5.0, V6.0, and V6.1, respectively). Similarly, the detection rate of Sentinel-3B rose from 64.3% (OLTC V2.0) to 71.4% and 75.0% in OLTC V3.0 and V3.1, respectively. Additionally, the cascade reservoir causing river channel expansion results in a better performance of Sentinel-3A in the Lancang River compared to the Nu River in the closed-loop mode (13.0% and 35.7%, respectively). Nevertheless, the considerable fluctuations in water surface caused by reservoir impoundment led to a wrong pseudo-DEM, resulting in poor performance of Sentinel-3 in reservoir regions before OLTC V6.0 was updated. The detection rate of low altitude, broad water surfaces (>500 m) decreased from 100% in a closed-loop mode to 0% in an open-loop mode, but increased to 100% in OLTC V6.0 and V6.1, respectively. The detection rate of high altitude, narrow water surfaces (<500 m) increased from 0% in a closed-loop mode to 40.9% in OLTC V6.1. Although the detection ability of Sentinel-3 is improving with the implementation of newer OLTC versions, the seasonal variations (usually more than 60 m) of water levels in reservoirs exceeded the size of the range window (60 m), rendering a complete measurement impossible.