This manuscript is addressing relevant scientific questions within the scope of Biogeoscience focusing on interactions between biological and chemical processes in restored seagrass environments. It combines benthic chamber, aquatic eddy covariance measurements and benthic fauna analysis on a chronosequence of four stages of seagrass development since restoration located within the same sheltered bay. It is well-written, and the methods seem adequate as does the analysis.

Nevertheless, to better compare your different stages of seagrass development, do you have any complementary information concerning their photosynthesis activity (e.g., PAM fluorescence analysis)?

My technical comments, mostly minor, are provided below:

Is your in-text citations based on relevance? Your preference isn’t so clear, sometimes your citations order seems to be chronological but not every time.

Methods: Explain more in details your alternative experiment location with your EC/ BC deployments to better understand your operating process (date, distances between EC and BC...) : add more information, for example in a table, about when and where (GPS data) you deployed your EC/BC systems.

Figure 1: Identify your subdivision a and b on your figure and describe your “Nat” abbreviation as it is described for the first time in a figure.

A figure describing your benthic chamber system could be added or at least a citation using the same system.

Modify your “bare” data color coding, e.g., fig3 not the same with your fig 2 and not so visible. Keep your color coding from your fig 2 and modify it even in your supplementary figure.

Line 100: Don’t you think you should also add Rodil et al., 2022 (https://doi.org/10.1002/ecy.3648), Rodil et al., 2020 (https://doi.org/10.1007/s10021-019-00427-0)?

Figure 3: delete “of” in your sentence: Linear regression between of oxygen and dissolved inorganic carbon (DIC)”

Line 381: A supplementary table showing all detailed PQ and RQ could be added to illustrate your explanation on high-variability.

Line 475: Quote your figure 6.

Table 3: You never quote this table in your text except in your discussion (line 522). You could either move it to your supplementary document or delete it.

Table 4: adapt your units as described in your methods part: molC m^-2.

Line 524: not useful to first compare your data with only one publication without the same methodology. Especially when few sentences later, you are doing a comparison with similar methodology.

Line 572: Z. noltii is now called Z. noltei

Line 605: a word is missing “to have a large range of photosynthetic pigments”.

Figure 7: Lateral import and export need to be documented or delete.

Homogenize your reference’s part, e.g. (line 767) do not use journal abbreviations.

Figure S1: add your site legend on your figure or into your legend. Homogenized your unit’s typography: modify wind speed unit m/s by m s^-1 and flow speed unit cm/s by cm s^-1.

Figure S2: Add subscripts to your O2 legend in y axis.

Please see my attached report below.

The article authored by Kindeberg et al. presents the results of a study aiming at exploring the role of seagrass meadows and associated biodiversity for carbon cycling at different stages of restoration process. The article, through the deployment of various techniques allowing for the measurement of oxygen and dissolved carbon fluxes as well as associated sediment and biodiversity components characteristics during the productive season, provides very interesting, and potentially important, results for a better understanding of seagrass ecosystems metabolism and functional effects of restoration actions. The article is well written and data analyses as well as subsequent  interpretations are appropriate and convincing. I therefore only made a few comments/questions for the authors, listed below:

-l157-178: Please give more information about the temporal sampling strategy. This temporal deployment strategy can indeed be deduced for EC measurements in figure 2, but this must be presented and justified already in the Methods section. Along the same line, have the BC deployments been carried out simultaneously (or kind of) with EC ones?

L213: Please specify what does exactly below ground biomass mean. All roots and rhizomes? Only living ones?

L220: In line with my just above comment, have the visible root fragments also been removed for the POC measurements? It must be specified because it can have implications for the carbon pools calculations in the case where only living roots and rhizomes would have been quantified as below ground biomass.

L256: please precise what does “absolute fluxes” mean. Averages of the three replicates?

L281: please introduce in the text the traits that have been chosen, and potentially the rationale for these choices relative to the research question. Were they all explicitly linked to carbon and organic matter cycling?

Figure 2 and lines 353-384: Figure 2 shows that flow velocities varied across studied patches. What are the implications of these differences for the surfaces (areas) of the footprint from which fluxes are integrated? Were these footprint areas comparable across patches? How did they coincide with the surface of the studied patches themselves?

L387-388: It is not clear whether this absence of significance also apply for below-ground biomass or not. It is important to precise this because, as shown in the table 2, BG core is clearly higher in the 7 yr meadow compared to either 3 yr and Nat. Along the same line, please indicate in the table the significant differences when there are, to help  the reader.

L438: bioturbation modes must be presented earlier, i.e. in the method section, see my comment above about traits.