I think that the authors have addressed most comments but I will need to look at the revised manuscript to make a final decision (Comment to editorial support: I think that as editors, we should always have access to the revised version of the ms at the same time as the answer letter, in order to properly make our work).
I suggest that the authors indicate in their report where in the revised ms have the changes been done to ease the verification. It will also help in future to separate the answers from the reviewer's comments with a "ANSWER" of something like that.
The comment by reviewer 2 "MODIS is mentioned here, but it is not indicated how it was used to support this argument" was addressed in the response report but I can not see if these explanations have been added to the ms.
As suggested by reviewer 2, explanations about 'key dates' are needed in the ms, because we cannot expect that the companion ms will be published early enough to access this, unless I missunderstood what ms the authors were talking about in their response (again this would not be an issue if I would have the revised ms at hand).
Best wishes for the following step.

Dear Authors,
Thanks for your revised manuscript. I only have a few more comments to consider:
1- You wrote at line 25: "Net changes in CO2 exchange fluxes are dominated by a major increase in photosynthetic uptake, resulting in a stronger CO2 sink in 2013–2015."
I think that the expression "CO2 exchange fluxes" is redundant (although I am not native English speaker). I think you need to choose one or the other between "CO2 exchange" or "CO2 fluxes".
2- You wrote at line 167: "Longer gaps were caused by flooding events, when the entire system needed to be shut down to avoid damage, and for a single event as a result of an additional laser offset in the closed-path gas analyzer at Tower 1 in 2015."
I think the second part of sentence (after comma) needs to be revised maybe as follows: "or resulting from a laser offset in the closed-path gas analyzer at Tower 1 in 2015".
3- What is this "previously" doing there at line 176?
4- You wrote at line 177: "This decision was based on our observance of implausible patterns in near-surface temperature measurements at our site, and as, because of a damped diurnal cycle, higher-quality soil temperatures at 0.08 m below the surface cannot be correlated to short-term changes in respiration patterns."
This sentence needs revision. I suggest the following but anything else is fine: "This decision was based on two factors: first, the patterns in near-surface temperatures were implausible at our site, and secondly, higher-quality soil temperatures at 0.08 m below the surface cannot be correlated to short-term changes in respiration patterns because of a damped diurnal cycle."
5- At line 184, I suggest: "For the statistical analysis of the whole dataset, a linear regression with a moving window of 14 days was used to analyze the peak uptake. An hourly shift was chosen to account for short-term variabilities."
6- I suggest the following changes in your sentence of line 188: "Measurements and thus errors are independent, the data are normally distributed and the variances are equal in most cases."
7- I suggest a few changes in the paragraph starting at line 380: "Here, we compare two observation periods, the historic (2002-05) and the recent dataset (2013-15), both covering three years of reference measurements. These timeframes might not be sufficient to fully represent conditions within each observation period, since surface-atmosphere exchange processes are often subject to pronounced interannual variability. Long-term continuous observations would allow a more in-depth statistical analysis. However, we observed characteristic patterns (e.g. the maximum CO2 uptake rate in summer) that clearly showed a distinctive trend between historic and recent periods. Thus, even from this limited database, we can see that the ecosystem has undergone a systematic shift over the past ~12 years."
8- At line 465, I suggest: "CO2 flux data from recent years indicate that the drained ecosystem has adapted to the disturbance, with changes in the biotic and abiotic conditions leading to a rebound to previous carbon flux levels."
9- At line 710, maybe replace executed by computed or obtained?
Best wishes for the last step.