The sensitivity of Doppler spectral indices (mean frequency, maximum frequency, spectral broadening index and turbulence intensity) to the conditions of spectral analysis (estimation method, data window, smoothing window or model order) increases with decreasing signal bandwidth and growing index complexity. The bias of spectral estimate has a more important effect on these indices than its variance. A too low order, in the case of autoregressive modeling and minimum variance methods, and excessive smoothing, in the case of the FFT method, result in increased errors of Doppler spectral indices. There is a trade-off between the errors resulting from a short data window and those due to insufficient temporal resolution.