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Calibration/Validation (C/V) studies using sites in the oceans have a long history and protocols are well established. Over lakes, C/V allows addressing problems such as the performance of the various retracking algorithms and evaluating the accuracy of the geophysical corrections for continental waters. This is achievable when measurements of specific and numerous field campaigns and a ground permanent network of level gauges and weather stations are processed. C/V consists of installation of permanent sites (weather stations, limnigraphs, and GPS reference points) and the organization of regular field campaigns. The lake Issykkul serves as permanent site of C/V, for a multi-mission purpose. The objective of this paper is to calculate the altimeter biases of Jason-3 and Sentinel-3A, both belonging to an operational satellite system which is used for the long-term monitoring of lake level variations. We have also determined the accuracy of the altimeters of these two satellites, through a comparison analysis with in situ data. In 2016 and 2017, three campaigns have been organized over this lake in order to estimate the absolute bias of the nadir altimeter onboard the Jason-3 and Sentinel-3A. The fieldwork consisted of measuring water height using a GPS system, carried on a boat, along the track of the altimeter satellite across the lake. It was performed at the time of the pass of the altimeter. Absolute altimeter biases were calculated by averaging the water height differences along the pass of the satellite (GPS from the boat system versus altimetry). Jason-3 operates in a Low Resolution Mode (LRM), while the Sentinel-3A operates in Synthetic Aperture Radar (SAR) mode. In this study we found that the absolute biases measured for Jason-3 were −28 ± 40 mm with the Ocean retracker and 206 ± 30 mm with the Ice-1 retracker. The biases for Sentinel-3A were −14 ± 20 mm with the Samosa (Ocean like) retracker and 285 ± 20 mm with the OCOG (Ice-1-like) retracker. We have also evaluated the accuracy of these two altimeters over Lake Issykkul which reached to 3 cm, for both the instruments, using the Ocean retracker. [ABSTRACT FROM AUTHOR]