Dear Dr. Borges,

Thanks for your responses to the reviewer comments.

Based on the positive reviews from two reviewers and my own reading, I am pleased to tell you that your manuscript can be accepted upon completing a (basically minor) revision, as you indicated in your responses, and as detailed in the following additional comments from me and a third reviewer who submitted comments following the open discussion phase:

1. Abstract
As both reviewers indicated, I also think that your quite long descriptions would present a big hurdle for readers to capture the main message. I would suggest you to shorten some sentences (e.g., section on mangrove creek data) and specify the objective of the study (We report a data-set obtained in the three branches (My Tho, Ham Luong, Co Chien)
of the Mekong delta (Bến Tre province, Vietnam) in December 2003, April 2004, and
October 2004, "to explore,,,,".

2. pCO2 unit
I am aware of the convention of reporting pCO2 in ppm. To facilitate comparison of data between different systems, however, I would use a more proper "partial pressure" unit or at least indicate at its first use why you opted for ppm.

3. Third reviewer comments
This review has arrived immediately after the closing of the open discussion, but provides many insights. Please consider these comments in you final revision.

The manuscript Carbon dynamics in the Mekong Delta by Borges et al. present a valuable dataset of importance to understand the carbon dynamics not only of the Mekong River delta but also the understanding of this dynamics in large river estuaries. However, there are a few points that should be considered that would help to make the manuscript more suitable for publication.
General comments:
The authors present data and discussion aiming to understand the carbon dynamics but information regarding, for example, the transport and degradation of carbon or factors controlling primary productivity is completely missing in the introduction. The manuscript introduction basically refers to CO2 and CH4 fluxes to the atmosphere, which is only a small part of the story presented. In section 2.1, despite the interesting and detailed information about geology and demography in upper basing, it is too long and most of this information is not essential for the manuscript. Instead more attention should be given to describe the carbon inputs from upstream the area, the vegetation, geomorphology, and hydrology of the delta and explaining where the delta starts. How the main channels differ from the side channels and mangrove creeks. Such information would be more useful to help interpret the results than social and economic information, which could be shortly mentioned in the introduction. Also, would be interesting to know how the tidal works in the area. How long time is each tidal cycle? What is the water level change in the mouth and in the most upstream site? Does the tide can significantly increase the residence time of the water?
In section 2.4 would be helpful for the reader if you explain the purpose of the mixing model informing what kind of information you can get from it and why this is important.
Despite the large list of papers regarding CO2 and CH4 fluxes from estuaries and large rivers none of them are mentioned in the discussion of section 3.4. Including this would improve the quality of the discussion. Most of the discussion is about the controls of pCO2, which was already covered before and perhaps some information presented here would be more relevant to the earlier discussion. In this section, the authors should focus the parameters that would be more directly related to fluxes such as pCO2, wind and water velocity. pCO2 and wind speed are the two inputs for the fluxes calculation and despite pCO2 was nicely detailed, the wind speed data was not even mentioned and information regarding water velocity other than discharge would be interesting to be included. Sawakuchi et al 2017 (Front. Mar. Sci. 4:76), Alin et al 2011 and Borges et al 2004, shown that in large rivers and estuaries k is dependent on a mixture of pCO2, wind, and water flow and therefore is site specific. In tidal areas, water velocity could change significantly depending not only the season but the daily with the influence of the tides. This should also be covered here.
To better show the spatial difference between main channels, side channels, mangrove creeks and the outer estuary. Statistical tests would be required to make the discussion more robust.
Specific comments:
Page 4, L21: April and Borges, 2004 is not in the References list.
Page 5, L30-32: The same information is presented in the description of the river and should be removed from the introduction.
Page 6, L1-6: This is also in the methods section. Perhaps it would be better presenting it just there and remove it from the introduction.
Page 7, L27-29: This could be replaced by densely populated
Page 9, L5-7: How much water was used and how it was collected and transferred to the serum bottles? Were there replicates? Consider the same for 13C-DIC.
Page 10, L22-24: Recent papers have shown that estimated k values for CO2 are different from CH4. Thus, a single model would not be the best way to tackle the flux estimates. If not possible to use different models for each gas, at least this limitation should be mentioned.
Page 10, L24-28: Please add here the atmospheric CO2 retrieved from NOAA and the distance from the station to the mouth of the Mekong River.
Page 12, L11-13: Please show the correlation between pCO2 and O2.
Page 12, L21-23. Please present the 13C-DIC values here.
Page 12, L23-25: What happens with other variables like POC, DOC, and TSM? The same discharge can be observed during the rising and falling water period, however, there will be different inputs of these materials depending if it is rising or falling waters. Furthermore, please consider adding in Fig 4 the channels and the outer estuary, similarly as you did in Figure 10.
Page 13, L4-5: Are these other tropical estuaries large systems, and where they are located?
Page 13, L5-7: Neither the O2 decrease or the pCO2 increasing patterns are not very clear in Fig 3. In April 2004 pCO2 increased from km 40 to 60, but then it decreased toward the mouth.
Page 13, L11: Please inform if the Phnom Penh is similar in terms of size/discharge to the Mekong
Page 13, L16-17: Considering this finding you could exclude the long-term change explanation given above.
Page 13, L22-30: You need to make a link to how all this information regarding these cations affects DIC and consequently pCO2. The way it is presented it seems out of context and does not contribute to the understanding of the C dynamics.
Page 14, L6: The Oct 2004 cruise you have samples collected farther out the mouth in the plume. This could be pure or almost pure ocean water and may be related to this very low pCO2 values observed. In addition later in Page 15, L5 you have mentioned that there was a phytoplankton bloom in the outer estuary.
Page 14, L14: Could the depleted 13 C signature in the DIC be related with a large input of C4 plant material?
Page 14, L17-18: What would be the expected 13C signature in the DIC from the weathering carbonate and silicate?
Page 15, L7: On page 14 L6 you say that the lowest pCO2 was 314. Which is the right value?
Page 15, L15-24: Seidel et al 2015 (Marine Chemistry 177,p 218–231) and Medeiros et al 2015. (Global Biogeochem. Cycles, 29, p677–690) may give you valuable information regarding this discussion.
Page 15, L28-30: Despite the trends observed in Fig 5 for the variables, these different patterns does not seem to be statistically significant. Please add the proper statistical tests results to make your point more convincing.
Page 16, L26-29: You have mentioned above that %POC, TSM and 13C POC in the side channels indicate large primary production. I am not sure if I got it right, but the model seems to not see the same trend, is that right?
Page 17, L10-13: If the side channels have lower water velocity than the main channels, higher sediment deposition is expected in this areas differently from the main channels were the water flow would wash out the fine organic sediment. If you have such condition then these shallow side channels could accumulate C fueling anaerobic degradation and CH4 production.
Figure 1. Add spatial scale bar and a North arrow.
Figure 3. Please consider changing the colored circles into different shapes. This would make easier to distinguish between rivers.
Figure 4. Would be interesting to see the channels and the outer estuary here as well, similarly to Fig 10.
Figures 5, 6, 7 and 9. Same as figure 3.