With this writing I am inviting the authors to submit a revision of their manuscript. I would like to remind the authors that when doing so they should reply to ALL reviewer comments and clearly indicate which action they took in response to each single comment. Possibly, I will send the revised manuscript to the reviewers for a second assessment.

Dear authors,

as both reviewers of the original submission had indicated that they would like to re-review the revised manuscript I sent it out for review again.

While one reviewer basically suggested to accept the revised manuscript as is, the other one was much more critical and in fact suggests that the revised manuscript is not acceptable for publication in its present form due to the fact that several issues raised by this reviewer earlier are still not taken into account properly and I concur with his/her opinion. I attach the reviewer comments below - the suggested modifications call for major changes of the manuscript, but are doable and will result in a more consistent and significant contribution to the literature. In case the authors decide to submit a revised version of their manuscript I ask them to carefully consider the reviewer comments and revise their manuscript accordingly.

Georg Wohlfahrt
Associate Editor Biogeosciences

Reviewer comments:
The authors did a good job trying to improve the quality and answer the reviewers questions. That said I still see some major issue that prevent the publication of this article:
1) I still strongly think that the CO2 part of the paper is minor and shadowing the interesting analysis on water. The authors refer to CO2 partitioning that is not discussed in the paper (just an equation, already published, is applied and no gapfilling) and also the very important link between C and H2O is however not addressed in the paper. So I still think that the CO2 part is just marginal (and with issues, see below)
2) In the Section 2.4.1 it is still not clear if the LRC is parameterized using all the data or only data with ustar above the threshold. In the first case this is wrong, because these data are known to be underestimated, in the second case the method would be not any more independent by FVF. However as stated above I suggest to remove this section and may be write a separate paper on CO2 where all these aspects are analysed. In fact the overall discussion is in my opinion not robust enough, ignoring uncertainty (are they really different? Did you check the overall uncertainty?) and proposing a method that removes a lot of data (see P9, L16-17) so increasing the uncertainty in particular as function of the gapfilling method used. Also it looks like there is still confusion on the ustar method and advection: working or not working ustar filtering was proposed and developed for advection and hilly terrains, saying that is not appropriate is wrong. May be not sufficient in some cases but again this needs to be shown and discussed.
3) I still think that the method should be part of a real validation and not a comparison between models or the use of measurements that are considered wrong in the paper (open path during rain). It means (referring to comments on Section 3.1.2 and answers) that the authors should find dataset were a close or closed path IRGA with heated tube is used and then apply the method developed to these data (e.g. adding artificial gaps) to validate the model and estimate the uncertainty. There are 600 sites in FLUXNET, a dataset like this is for sure available.

I accept the current version of the manuscript pending to the following technical corrections (not requiring further editor assessment):
(1) p. 3, l. 22, p. 3, l. 24, p. 4, l. 1: (and CO2)

The following suggestions are meant to make the structure of the paper conform with the classical structure of scientific publications:
(2) p. 7: I suggest section 3 should be entitled "Results and discussion"
(3) p. 9: following on with (2) I suggest section 4.1 to be renumbered as 3.3 and entitled "Application: Wavelet coherence ...."
(4) p. 9: to fit with the above change, I suggest to remove the first line on p. 9 and start the sentence in line 2 with "In the following we illustrate ...."
(5) p. 10: section 4.2 should be numbered 3.4 and the title changed to "Application: "Water use ..."
(6) p. 10: section 5 should be numbered as section 4