The TOPEX/POSEIDON altimeter measurement system is evaluated for the first 46 repeat cycles (September 23, 1992–December 23, 1993) using tracks over the Great Lakes. The temporal variations in lake level are removed from the altimeter measurements using in situ lake level measurements, thus permitting the performance of the altimeter system to be assessed. For the NASA altimeter, the root‐mean‐square (RMS) scatter of the residuals is 3.95 cm using all the tracks over the lakes. However, some of the scatter in this result is probably due to lake tides or seiche, which can amount to a few centimeters amplitude near the ends of the lakes. When the seven best tracks are used, which cross the center of the lakes where tides/seiche effects are minimal, the RMS error is reduced to either 2.9 or 3.0 cm, depending on whether the Centre National d'Etudes Spatiales (CNES) or NASA orbit is used. This places an upper limit on the error budget of the altimeter system, excluding ocean tides and inverse barometer effect. There are several short‐period variations in the residuals. The most pronounced is a 55‐day period, with a 1‐cm amplitude, which we believe is (at least in part) due to orbit error. When the model‐derived wet tropospheric correction is substituted for the TOPEX microwave radiometer correction, the RMS error increases significantly, possibly resulting in an annual cycle of a few centimeters. Evaluation of the ionospheric correction indicates that the dual‐frequency correction provides an average improvement of 0.85 cm over the Doppler orbitography and radiopositioning integrated by satellite (DORIS) correction. Although there are insufficient data to directly assess the CNES altimeter, the relative bias between the altimeters is estimated to be either −14.3 or −15.6 cm (NASA altimeter measuring short), depending on whether the DORIS or dual‐frequency ionospheric correction is applied to the NASA altimeter.