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The problem of minimization of errors in water level retrieval for the Volga reservoirs from altimetry measurements can be resolved by retracking Jason-1, 2 satellite altimetry data. For justification of the optimal retracking algorithm average impulse response of a statistically inhomogeneous surface was calculated theoretically for a model of the terrain in the neighbourhood of the reservoirs. The modeled waveforms are in good agreement with Jason-1, 2 waveforms for the same area. Comparison of the data with in situ measurements shows that retracking significantly improves measurement of the water level. General principles of the retracking algorithms for complex areas (land, coastal zone, inland waters, etc.) based on calculations of the waveforms taking into account statistical inhomogeneity of the reflecting surface adapted to a certain geographic region, are discussed.