The eddy covariance technique has been widely used to measure turbulent fluxes between land and atmosphere. However, the influence of vibrations of the tower and mounting arms on temperature variances and fluxes still needs to be examined. Here, this manuscript examines 30-min average temperature variances and fluxes determined by eddy covariance systems including Campbell Scientific Anemometer Thermometry (CSAT3B) with closely co-located fine-wire thermocouples along with LI-COR CO2/H2O gas analyzers at multiple heights above a sagebrush ecosystem. It is found that temperature variances and fluxes are underestimated by using sonic temperature (Ts) in comparison with fine-wire thermocouple temperature (Tc). The less energy of Ts spectra in the low-frequency range causes smaller variances and fluxes of Ts than Tc. The manuscript further investigated the potential causes for the discrepancies between variances and fluxes of Ts and Tc,  and concluded that underestimated temperature variances and fluxes by using Ts are likely caused by wind-induced tower vibrations. These results are of great significance for improving our understanding when we calculate turbulent fluxes.

The following are a few minor comments I have on this manuscript:

1.     This study aimed to address a potentially important issue associated with eddy covariance measurements. It would be highly beneficial if the manuscript could include recommendations and to help explore and improve the potential issues caused by vibrations in future experiments.

2.     This study used the measurements of Ts and Tc at three heights of 40.2, 23.0, and 12.8 m. Would the results remain consistent if data from other heights were utilized?

3.     How were the tower and sonic anemometers installed, was the tower guy wired, were the poles used to attach the sonic anemometers to the tower installed horizontally or vertically.

4.     The results in Figure 7 are only shown for the measurements at 40.2 m. How about the results at the other two heights?

5.     Line 258: “According to the comparison of the T_s and T_c spectra, the whole frequency domain can be divided into three regimes…” Probably replace the word “regimes” with “ranges” or “zones”.

Gao et al., utilizing multi-level co-located sonic anemometers and fine-wire thermocouples, compared the difference between temperature variances and fluxes derived from sonic anemometers and thermocouples and investigated the potential causes for the observed discrepancies. They found that temperature variances and fluxes determined from the sonic anemometers were underestimated in comparison with the counterparts determined from thermocouples, mainly attributed to the lower spectral energy in the low-frequency range. They concluded that the observed underestimation in temperature variances and fluxes determined from sonic temperature was likely caused by wind-induced vibrations of the tower and mounting arms.

The topic is interesting and is of great significance in the eddy covariance community. My comments are as follows:

1. My major comment pertains to the conclusions of this paper. The author concluded that the temperature variances and fluxes determined from sonic anemometer were underestimated which is likely attributed to the vibration and mounting arms especially in strong wind conditions. Besides, CO2 variances and fluxes were sensitive to such uncertainties. However, the paper does not specify which temperature product, the sonic-derived or thermocouple-measured, is more reliable. It would be beneficial if the author could provide recommendations on the preferred temperature product to be used in investigating long-term CO2 budget and energy balance closure. Can the author provide suggestions to reduce such uncertainties in scalar flux calculations?  
2. As shown in Figure 1, there are 8 levels of measurement on the tall tower and four levels of measurement on the short tower. Is there any reason for utilizing only three levels of measurement (12.8, 23.0, and 40.2 m)? Would the results remain consistent if measurements from other heights were used? It would be interesting to compare the data from 6 m (short tower) and 8.2 m (tall tower) since small wind speed differences are expected between these two heights. As a consequence, the influence of wind-induced vibrations of the tower and mounting arms on sonic temperature might be highlighted due to different tower structures and mounting arms.
3. Figure 7 only shows the results at 40.2 m, can the author provide results at the other two heights?