The article by Knutson et al provides some descriptive data of Carbon dynamics in aquatic systems undergoing permafrost thaw. The article is well structured and while it does not tests any clear hypothesis or concept, it provides a useful description of data in an important region undergoing rapid changes. The article could be sharpened with more clear research questions, which I detail below.

One major issue I would like to bring up and that the authors do not mention is the role of the redox scale in explaining the patterns here. The authors have a large gradient in SO4, linked to pH and DOC, that is clearly connected to the low CH4 concentrations in the stream, and a more clear exploration of this resolution would be a nice contribution of the paper. If SO4 is abundant then is not energetically favorable to produce methane, so this could explain a lot the patterns regardless of the system.

MINOR COMMENTS

L15: The second sentence  starting "at the Iskoras site in Northern Norway..." feels a bit rushed to introduce the methods part in the abstract, presenting the knowledge gap or question before would help the reading.

L24: It is maybe better to keep the abstract with one paragraph.

L53: the formation "of" thermokarst ponds. Missing an "of".

L83: The introduction is overall good, but there is an abuse of "these" and "their" (10 in this page), which makes the reading a bit hard with the indirect references. Having a more direct writing would help the reader, and some of them are unknown what they refer to.

L99: I would make those critical questions more explicit.

L102: And the gaps are also not specified. This should be way more explicit.

L109: Where is this OM mobilized from? Permafrost thaw? Recent GPP?

L126: What does the +/- refer to here?

L165: Would be helpful to specify what those measurements are for, at least for "dark incubations".

L178: The ions need their plus and minus

L197: The calculations for CO2 are very unclear. If samples are acidified, all DIC becomes CO2 before the shaking. Was this done for all samples or one set for DIC (acidified) and the other for CO2 (not acidified)?

L200: write 15 instead of text.

L240: Change "processing" to production.

L303: "SAR" is introduced here for the first time, this needs details in the methods.

L309: conductivity is commonly    expressed as microsiemens/cm, so this would be a better unit.

L366: Here the DIC and CO2 plot are repeated, one should be changed.

L422: It is a bit confusing to say "fresh OM input from themokarst development", as is probably "old carbon. Same in line 434.

L448: What do you mean CO2 is sequestered here? May need a bit more explanation.

L446: I am not sure there is support for the carbonate inputs sustaining CO2 from streams here. 

L471: same here, groundwater can be rich of bicarbonates but also directly CO2, which is highly enriched in the groundwater. I would leave the discussion more broadly defined with DIC instead of getting into the weeds of the carbonate equilibrium here. A missing reference would be some more stream continuum focused, such as Hotchkiss et al 2014 (Nature Geoscience).

L496: Same here, the mention of weathering is a bit off without data on that.

The manuscript « Water chemistry and greenhouse gas concentrations in waterbodies of a thawing permafrost peatland complex in northern Norway » presents original data of greenhouse gas (GHG) concentrations in water bodies from a peatland area in the permafrost region in Norway collected over 2 years of monitoring. The dataset for the GHG is highly valuable for the community given the little knowledge on these emerging environments. The data are accompanied with water chemical composition, but some additional information is needed before these additional data can be used in the manuscript (see comments below). I would really encourage the authors to address the comments below to allow the publication of this highly valuable GHG dataset.

Major comments

The most important comments are about the water chemistry measurements (sampling, analytical procedures, and data availability).

Firstly, according to the method description, the unfiltered waters were sampled in HDPE bottles and kept at 4°C until analysis. The method does not specify whether filtration was performed. For the analysis of SiO2, SO4, NO3, NH4, totP concentrations, if filtration was performed, it should be specified with what type of filter (material), what pore size, and how long after sampling. For DOC and POC analysis, the information about filtration should be more specific and specify which type of filter, pore size, and how long after sampling. Importantly, for the analysis of SiO2, SO4, NO3, NH4, totP concentrations, if no filtration was performed, I would strongly recommend not to use the data, and to focus the manuscript on the C cycling. Unfiltered waters may contain small sized particles which continue to interact with the dissolved phase after sampling (dissolution, adsorption, etc). This is why it is conventionally recommended for this type of water analysis to filter within 24h to 48h.

Secondly, for the analysis of the water samples, the authors refer to a report by Vogt and Skancke, 2022 for the description of the analytical procedure and quality control. The report is freely available online (in Norwegian, which means this is not accessible to the international readership). From what I could see in that report, there is no mention of SiO2 measurement. If these data are included in the manuscript, the analytical procedure (instrument, detection limit, precision) for all the parameters measured on water samples including SiO2 should be included in the manuscript to be accessible to the reader. Regarding the measurements of dissolved silicon concentration (sometimes expressed as SiO2 in mg/l), the authors should refer to SiO2 concentration and avoid the use of the terminology silica. Because silica corresponds to the solid phase.

Thirdly, the method section refers to alkalinity. There is no information about how this was measured. The caption of Table 3 specifies that for this study DIC is considered as the sum of dissolved CO2 and bicarbonate. There is a need for more precision on the methodology and for the use of a similar terminology throughout the manuscript to avoid any confusion. And there is a mention for TOC analysis in mg/L. The TOC is usually used to refer to the total organic carbon concentration in a solid phase. What is the TOC for the water? This should be modified and redefined.

Fourthly, the manuscript is based on a large dataset of water samples collected over two years, and median values are presented in Table 2, but a full access to the individual dataset should be made possible to review the manuscript.

Comments by sections

Abstract

L18:  the authors use the terminology of “organic acidity” to refer to “organic acids” as a driver for the pH. This should be revised, and the terminology “organic acidity” should be removed from the manuscript (L18, L20, L318, L497, L516).

L27-28: check that the 4 is as a subscript for CH4

Introduction

L35-36, L40: the authors should incorporate recent publications with the permafrost carbon pool on land of 1460-1600 Pg C, and specify that they refer to the permafrost instead of northern latitude regions (Meredith et al 2019, IPCC Special Report on the Ocean and Cryosphere in a Changing Climate; Schuur et al 2022, https://doi.org/10.1146/annurev-environ-012220-011847; Strauss et al 2024, https://doi.org/10.1016/B978-0-323-99931-1.00164-1).

L112: the motivation of the paper is the C cycling, and this is highly relevant. The justification for the need of the other parameters being measured on water should be clarified (also see major comments about the clarification needed for the analysis).

Methods

L145, and L165: specific information about the number of water samples collected in each waterbody, the date, the time of the day (relative to the precipitation events) should be provided in details. For the data presentation, the number of data included (n = X) should be specified.

L171-191: see earlier comment as a “major comment” about the water chemistry section

Results

L287-333: The first section of the results should be re-structured to present the data step by step, and to move the part related to the interpretation of the data to the discussion. This section should consider the major comment about the methods to define the parameters that will be described in this section and presented in Table 2 and in Figure 2.

L291: “at the top” of what?

L293: “end of the curve” – which?

L296: this is for the discussion section

L299-300: The method section specifies that the totN data will not be presented for a reason, so there should be no mention of these data in the results and discussion

L306: “somewhat higher” should be more specific with statistics

In Table 2: NO4 should be NO3

L319-321: this is for the discussion section

Figure 3: specify in the caption that this is dissolved concentration in CO2 and CH4 in waters. There is no description of the lower panels.

Discussion

L425-459: in the second section of the discussion, there is not link to the data of the present study. The discussion should compare the original data and discuss them with the literature. Also the title of the section should specify what part of the water chemistry will be discussed in the section.

Section 4.3: references to the data presented in the results should be included by adding a link to a figure or a table at L461, L468, L475.

L511: variability of what?

L538-540: Data availability: the manuscript is based on a large dataset of water samples collected over two years, and median values are presented in Table 2, but a full access to the individual dataset should be made possible to review the manuscript.