The manuscript “Fate of dissolved organic matter across the permafrost–nearshore water continuum: role of the intertidal sediments” by Flamand et al. reports on the important issue of land-ocean constituent transport induced by permafrost thawing and erosion. As such, the topic is very relevant and ties in two themes of which not nearly enough is known to date, namely organic carbon release from permafrost and subsequent processing underground within subterranean estuaries.

The data appears to be of good quality and the manuscript is overall well written. However, I still have some major concerns that should be addressed before the manuscript can be accepted for publication in Biogeosciences. Mainly, these entail the way the overarching theme, and later the data, are presented to support the proposed story.

Major comments:

The English syntax and grammar are often awkward or incorrect. The manuscript should be thoroughly checked before re-submission, either by a native English speaker amongst colleagues or a professional editing service.

The introduction is in parts unclear, especially regarding the influence of tDOM on coastal ecosystems. Does tDOM strongly influence the arctic marine ecosystem or does it get strongly removed and only a small fraction remains? At which point does the major turnover take place in the land-ocean aquatic continuum?

As a non-expert in permafrost biogeochemistry, I also found it difficult to understand the land-ocean aquatic continuum (if it can be called continuum, even) across permafrost-fringed coastlines. How does water transport mainly take place, via surface runoff or thawing and groundwater transport through permeable sediments? How might the impact of permafrost differ when it is delivered through (i) rivers, (ii) erosion and direct deposition into the ocean, and (iii) STEs?  This aspect of the hydrology of the investigated locations is not well characterized yet. Figure 1 does show a bit of the sampled environments, but it is too superficial. The diagram in the graphical abstract should be adapted in a new Figure 2, for example (2A) to elaborate on the different flowpaths and permafrost delivery mechanisms to the coastal ocean, and (2B) to depict sampling points of this study.

Finally, provocatively speaking: Does STE processing (quantitatively and qualitatively speaking) even matter in this environment? What do STEs do here that other interfaces can’t? Redox fronts with potential iron curtains are named as major modulators, but iron distributions in the STE are not reported in the manuscript. What are the natural Fe-DOC ratios? What is the pH? Is there any information on sediment composition which might enhance OM adsorption, perhaps from earlier publications?

Figures (general comment):

Some Figures are in color, while others are only black and white. Just fully commit to color – most people read the papers online anyways. Figures 4 and 7 also have very small fonts. I don’t recall ever seeing salinity denoted as “Sp” before. Overall, the figure captions don’t describe all variables in the figures, so please provide comprehensive information there.

Tables:

There should be an additional table with environmental data (including iron, temperature, oxygen saturation) of all samples. I don’t want to have to download everything from PANGAEA to understand the system.

Minor comments:

Lines 16-18: The introduction of iron hydroxides and groundwater comes a bit abrupt after a generic phrase of “multiple fates” of DOM. The two sentences could be harmonized better to introduce first permafrost and then mention underground transport and its specifics as one of the pathways.

Lines 23-24, and throughout the manuscript: Maybe I didn’t find it in the manuscript but how can mineral-DOM interactions be disentangled from microbial processing? The former will target humics and “protein-like” material will remain so it might resemble microbial turnover and DOM production by selective retention.

Line 43: “60% of the world’s carbon”, is that correct? That would include inorganic carbon, no? Please clarify.

Lines 49-52: Add examples for permafrost. Does it supply something specific, i.e. a certain nutrient species or amount, that supplements/influences oceanic regimes?

Line 53: On which time scale is “rapid”? Are there any reference values for volumetric water fluxes from permafrost?

Lines 56-59: Like above, be more specific on how tDOM influences all these (or at least one of them) with an example or two.

Line 63: All throughout the riverine catchment? Or only in the estuary? Again, please be more specific if that information is available in the cited paper.

Line 66: Are there any estimates or examples to back up the statement about a strong tDOM influence on the arctic marine systems?

Lines 72-73: Why and where do these iron curtains form?

Lines 75-77: STEs are complex everywhere in the world. The introduction of STEs here is a bit uneven and should be clearer, especially for a permafrost audience who does not know the term.

Lines 77-78: “Its role (…) could be a key zone”? Please rephrase.

Line 80: “affinity with amorphous Fe-hydroxide in STE” sounds awkward. Please re-phrase/clarify.

Line 86: “Recent findings (…) characterized permafrost-derived DOM as LMW, proteinaceous” but later in the manuscript it reads as if the cited paper reported DOM as HMW humic-like (lines 337-339). The contradiction should be explained in more detail.

Lines 91-97: The rationales and aims are rather vague. I’m assuming that the study was planned with an expected outcome in mind. These expectations form the hypotheses and questions and should be mentioned here more clearly.

Line 94: Is that site-specific scale approach discussed later? Because I don’t think I found it again in the results & discussion.

Line 118: What is an “important lagoon system”?

Sections 2.1 and 2.2: As mentioned in the major comments, site and sampling descriptions would vastly improve from the addition of a schematic diagram, for example in the form of a cross-section depicting the coastal topography, location of permafrost layers and vegetation, mean water line, sampling point locations etc. At least this should be done for the high-resolution sampling site Kugmallit Bay. Two of the sites are located near a large river, was it sampled as well as an endmember? The river is mentioned in results & discussion for the first time which is too late. What are the tidal conditions? All potential endmember characteristics should be outlined in the introduction or site description of the methods section.

Line 153: The TOC-VCPN from Shimadzu is all capitals.

Line 155: µM here, but µ mol L-1 in the figures – please unify.

Line 173: What is significantly different? Was a statistical test performed to come to this conclusion?

Line 181: Consider calculating BIX to complement HIX in the revision, since tDOM transformation from one to the other is one of the proposed mechanisms.

Section 2.5: Was pH monitored? It governs Fe-DOM precipitation and was likely changed during FeCl addition. Consider repeating the experiment if you have backup samples, if only for a pH check.

Lines 209-210: What is the main factor influencing the salinity in the seawater? Groundwater or surface runoff and rivers?

Line 2019 Waska et al. 2021 does not take place in a microtidal environment.

Line 220: “the tidally input of oxygen is rapidly consumed” sounds weird. Please rephrase.

Lines 235-238: Yes, conditions in the STE are well-suited for transformations, but the groundwater endmember does not seem to stem from in situ meltwater. So, it could be from anywhere inland with unknown water ages, and might have been transformed extensively before entering the STE.

Lines 241-242: Does Figure 4 depict all samples from all sampling sites? The symbols should be color coded to disentangle different sites and perhaps even locations on the beach (upper vs. lower).

Line 251: What is “negatively decreased”?

Line 256: “The relationships in between is used” – not sure what that is supposed to mean – please clarify.

Lines 266-267: Not necessarily if other processes like adsorption affects CDOM more, then both can be simultaneously decreased but by different mechanisms, no?

Lines 285-290: An increase in aromatic DOM could also result from degradation of particulate organic matter within the STE.

Line 290: There is BIX! But where does it come from? A different study? Can the data be compared? Why is there no BIX for the present study?

Lines 292-297: I don’t follow the reasoning here. What is the autochtonous DOM in this story here? The optical parameters in Fig. 5 are not stable in seawater. They fluctuate quite a lot and have varying CDOM/DOC ratios. Assuming low temperatures and high freshwater fluxes they might just be the result of two endmembers (direct permafrost input and Mackenzie River).

Lines 303-305: To support this statement, Fe distribution and dynamics, and tidal range/extent of beach inundation of the study sites need to be reported in sufficient detail.

Lines 306-327: Can you add the CDOM/DOC ratios of the samples before and after Fe addition, so that they can be compared to the natural ratios depicted in Figure 5?

Line 338: shift from past to present tense, please be consistent

Line 339: Add more environmental and thematic context for the cited paper to support the comparison.

Line 345: Same as above, was that done at the same study sites? Why are related studies cited so late in the manuscript? They should be used in the introduction to set the stage for the story presented here.

Lines 348-350: Does this statement refer to the Chaillou et al. 2024 paper or the present study? It would be odd to finish results & discussion with a conclusion from another paper.

Line 354: “would be”?? Also, I thought that microbial degradation does not favor humic-like material.

Line 358: “submarine groundwater discharge”

Figures:

Graphical abstract: The dots in the left scatter plot are really small, as is the font size of the axis numbers.

Figure 4: Use colors, make the font bigger, denote different sampling sites if appropriate, add units to the boxplot axis titles.

Figure 5: Is “S” Salinity? It was “Sp” in Figure 4. Also, why are some symbols light grey which is not part of the color scale?

Figure 6: Use colors, and perhaps another chart type or design. For the majority of symbols in B) it is impossible to decipher any information. Consider adding a third graph depicting DOC/CDOM ratios, and adding a range of these ratios in Figure 5 for reference.

Figure 7: See comments for Figure 4.

Apologies for the delayed review! It took more time than originally anticipated...