A water level measurement radar estimates beat frequencies to extract the corresponding water level information for water resource management. Therefore, it is required to maintain the high degree of reliability and accuracy in beat frequency estimates. However, Beat spectra of water surface return echoes can have very widely varying shapes according to system frequency linearity, measurement environments and weather conditions. Therefore, serious problems may arise in maintaining the reliability and accuracy of the conventional level estimation method. Therefore, in this paper, high resolution spectrum estimates are analyzed for improvement of the conventional method. These methods show that the more accurate level measurement can be possible on the condition that SNR is higher than a certain required threshold. However, if SNR is too low, the conventional method shows that estimates are more reliable than the suggested method though absolute errors are too large.