The authors present a comprehensive data set on CO2 fluxes and carbon balances for a series of managed Dutch peatlands with the aim to address possible mitigation effects from subsurface water infiltration systems. This is an excellent and well elaborated study in terms of applied techniques in the field and in the statistical section, as well as in the depth of data analysis and interpretation. I strongly recommend the preprint to be published as full paper in Biogeosciences after consideration of the comments below.

General comments

Abstract. Please provide an estimate on the potential of WIS to reduce peatland emissions in the Netherlands.

Line 51. Please explore in the discussion whether the target of -95% by 2050 could be reached with WIS.

Line 102. I suggest to explore the presence of clay on top of the peat layer in the introduction – how frequent are these situations in the Netherlands, how may a clay horizon affect the CO2 balance when the water table is raised etc. Many readers may not be familiar with this type of soil.

Methods: Do sites contain inorganic carbon? If so, this should be mentioned at some point.

CO2 measurements. At site Zegveld the control is compared to two different chamber types; how does this influence the interpretation of results?

Lines 220ff. Please provide a (supplementary) figure or an error estimate for predicting Reco from temperature for the individual sites.

Line 228. Sentence starting with ‘We partitioned’ belongs to the beginning of para 2.2.4.

Line 310. Useful approach.

Line 413. This is a very relevant finding and should be presented also in the abstract.

Line 419 ff. Authors present results for alternative regression models but it is not explained what to do with this finding.

General: The MS would benefit from showing the year-round GW measurements in a supplementary figure (and not only aggregated as in Table S1) as this would visualize the effect of WIS.

Points to be included in the discussion section:

Line 297. DOC and other pathways were not considered, which is acceptable given the efforts to estimate those terms. However, leaving them out from the overall budget calculation implies that the observed net C losses from the studied systems might be actually higher. This should be discussed later, together with literature estimates from similar systems (if available), denoting the possible magnitude of this effect.

Data in Fig. 6 show that manure affects the NECB. How much manure is produced from the harvests per site and how much would therefore be available to improve the NECB? This is more than a theoretical question as a the effect of manure on the ecosystem’s C budget is now accounted for elsewhere.

You discuss why are NEE/NECB results are so different to Tiemeyer et al. 2020. Could the clay layer also play a role? The SOC within the clay layer may be less prone to decomposition as unprotected peat, for example.

Technical remarks

Line 68. Please update references Buzacott and van den Berg.

Line 68. Sentence not complete. They mean a change from conventional agricultural land use towards what?

Line 75. Please add: ‘as the hydraulic conductivity of degraded peat soils is…’

Figure 2. I suggest to replace the grey bars for the WTD by blue bars or another colour providing better visibility. The figure provides C concentrations in kgC/m3; this is a C density, a C concentration would be kgC/kg soil.

Figure 4. Please revise so that either dark and light red is replaced by a different colour.

Line 328. Please move first parenthesis before ‘2022’.

Figure 9b. I suggest to use also different symbol types, not only different colours in this plot.

The manuscript is based on an impressive dataset and is clearly written and good English language. This kind of information on the effectiveness of GHG mitigation measures on peat soils and methods to estimate the emissions based on environmental variable is urgently needed.  Comparison of the WTD-NECB relationship in different datasets (Fig. 9) was especially interesting in this manuscript. I have only minor comments.

Title: I’m not sure if the title should start with ”Using automated transparent chambers to quantify…” as this was not a methodology-oriented paper to my opinion. I would stress the large dataset by including the number of sites and probably ”continuous measurements” in the title if needed. Could it be: CO2 emission reduction potential of water infiltration systems at six drained coastal peatland sites in the Netherlands.

I think the infiltration system you used is also called submerged drainage. If this is true, please also include this term in the methods section to make it clearer for readers who are less familiar with (Dutch) drainage systems.

In order to understand the functioning of the WIS, a figure on the WTD variation within a year would be useful.

Table 1: should the title in the 6th column be ”ditch WTD”, not ”aim”.

Line 347: is-->was

Line 370: add also the mean value (all sites) for NECB.

Line 412: This kind of observations on the proportion of C lost annually do not widely exist. You could add it to the abstract.

Line 478: Paludiculture is not a water management system but a cultivation system. You could even use WIS to raise the WT for paludiculture (if possible to raise the WTD to 20 cm). I suggest revising this sentence e.g. to: Apart from WIS, typically leading to moderate WTD increase, more efficient WTD regulation could be implemented to allow paludiculture (Geurts et al., 2019; Martens et al., 2023) or restoration to a full peat growing ecosystem (Nugent et al., 2019).