This manuscript presents a year-long dataset of GHG concentrations and fluxes from 5 headwater catchments in Germany from streams, agricultural ditches, and WWTP outflows.  It identifies controls on GHG dynamics using mixed-effects models and structural equation models. In addition, it upscales flux rates to calculate annual emissions in terms of global warming potential. The main finding, that anthropogenically impacted streams have higher and more variable GHG concentrations and fluxes, was well supported. Overall, the manuscript presents results that will be an important contribution to our understanding of GHG emissions from inland waters and I find the analysis and results novel and worthy of publication.

I have a few suggestions, although they mostly minor and easy to address.

Abstract:

-I don’t think that the analysis backs up the statements about separating in situ production of GHGs and direct inputs of GHGs (e.g., ln 27-28, 30-31). These statements should be removed or rephrased. 

-I think the authors should more clearly state that anthropogenically impacted streams have not only higher, but also *more variable* GHG emissions than natural streams in the abstract. (i.e., give some sort of variability stats)

-I would consider mentioning some of the other main findings in the abstract (if possible within word count limits): 1) the break down of the expected stream-order patterns in impacted sites and 2) the finding that CO2 is the dominant contributor in terms of global warming potential

Methods:

-I don’t see temperature/seasonality or NH4 in the SEM results, even though these parameters are listed as input variables.  Were they found insignificant and dropped? Please clarify.

Results:

F2. Consider using colors to represent major land-use classifications and shades to differentiate the sub-classifications. For example, crop, crop + settlement, and crop + settlement + WW inflow could be given different shades of the same color. Also, yellow is somewhat difficult to see on all these plots.

I don’t have the background to fully assess how the SEM analysis was applied but it seems to make sense and F5 is great.

I find the conclusion that typical stream order patterns break down in anthropogenically impacted streams interesting (L573-584).  However, I don’t see the data presented in the results section. Please include it here (and perhaps add to the abstract as well).

Discussion:

Consider discussing the result that CO2 was the main contributor when emissions of all three gases are converted to CO2 equivalences (F6).  I found this result to be interesting and perhaps it deserves more attention in the manuscript.  

Conclusion:

L620 - It seems like CH4 is also higher in the anthropogenically impacted sites?

Minor:

L40 – “contributors to global greenhouse gas budgets” or “contributors of greenhouse gases”

L41 – Li et al., 2021 citation only refers to headwater streams

L52 – “in situ N2O production”

L70 – “where”

L260 – “May 31”

L369 – consider using uatm for N2O, instead of natm, as it is more commonly used

L375-376 - It looks like negative fluxes are actually presented in F3.

In general, this is a very nice study design and thorough sampling and analysis. I do not see any issues in that regard. While most comments are minor, it does seem that the introduction and discussion sections have received less attention, and are currently quite superficial in some sections, and overlook or mix up some concepts/terminology. So while I like this study overall, my comments below highlight the need for the authors to dig a bit deeper in their framing and interpretation of the work relative to other work in the field. I support this paper being published if the authors can fix these issues. 

General comments:

Issue with lateral inputs in introduction: Up to line 62, nowhere in the paper to this point is lateral transfer of GHGs mentioned. It is especially important for CO2 in headwater systems, but in the drainage ditches, the GHG production in the wetlands themselves must be a huge fraction of the emisisons budget, no? The introduction needs to more thoroughly reflect this aspect of mechanistic control.

The overview pgph in the intro line 75 and on is pretty thin on mechanistic insight. Please integrate lateral inputs of GHG more carefully, aside from one sentence, it is all about internal production. How do storms and seasonal changes in hydrology alter the balance between catchment CO2 loading and internal production?

Discussion section 4.3: This section should be expanded. We need a more thorough numerical comparison with other studies.  There needs to be a conclusion, what is special or new about your study compared to those papers? Anything unique here? What can you say overall about the land use sites vs non?  I think that more work needs to be done in this section to take what is a very nice dataset and analysis, and actually make it impactful in terms of the insights that you are providing the community.

Line by Line comments:

L 29-31 - is it in situ, or is the ditch draining a landscape that has a lot of GHG production? This would be adjacent source, not in situ in the ditch.

L33-34 - but natural systems make up a huge fraction of the total global stream area, so if your goal is to simply scale the contribution of streams, then your reasoning is not accurate. I'd refocus the implications here and say something more generalizable about why emissions research in these impacted rivers are important.

L37 – In this figure, No indirect effects on GHG in this diagram in anthropogenic domain. Nutrients, hydrology, etc will also modify emisisons patterns indirectly.

L43 - photochemical DOM processing too.

L48 – conclusion sentence needed.

L58 – compared

L69 – numerical context needed.

L70 – in rivers linked to land use, or direct land use emissions? Be specific here.

L64-74 - here, integrating the important discussion points from key articles would strengthen your introduction. I list a few but there are also more: 

Park JH, Nayna OK, Begum MS, Chea E, Hartmann J, Keil RG, Kumar S, Lu X, Ran L, Richey JE, Sarma VV. Reviews and syntheses: Anthropogenic perturbations to carbon fluxes in Asian river systems–concepts, emerging trends, and research challenges. Biogeosciences. 2018 May 17;15(9):3049-69.

Begum MS, Bogard MJ, Butman DE, Chea E, Kumar S, Lu X, Nayna OK, Ran L, Richey JE, Tareq SM, Xuan DT. Localized pollution impacts on greenhouse gas dynamics in three anthropogenically modified Asian river systems. Journal of Geophysical Research: Biogeosciences. 2021 May;126(5):e2020JG006124.

L72 – constrained

L74 – through this part of the intro, this terminology or contrasting of urbanization and land use is confusing. Do you mean point- and non-point pollution impacts? Or by land use do you mean agricultural land use specifically? Please clarify.

L89 - this point could be reworded. It is essentially saying that low sampling frequency does not capture short term variability in GHG cycling. This is obvious, so could you take this line of thinking a step further?

L91 (and more general) - this statement is not exactly defensible. People have been measuring stream GHG patterns for decades. Note that the oldest reference cited here is 2018. A deeper exploration of the literature here would be needed to pinpoint more specific unknowns about riverine emission patterns. At the same time, much of the issues in this pgph is already presented in the last one discussing sub-annual patterns. Consider just removing or really going much deeper.

L209 – detail standards used for GC calibration.

L278 - Terminology "end" and "exogenous is misleading throughout, because things like water temperature are within the system, so to me are not exogenous. Why not call them 'substrate' and 'environmental conditions' or something? This comment applies throughout the paper where this framework is used.

L305 – fold

L337 - throughout the water chem and GHG results sections, when something is significant or not, please report the test statistic in the text.

L407 - either mention that the scales are not the same between the 3 columns, or preferably log transform the Y axis and use a consistent scale to facilitate comparisons between catchments.

L460 - the light blue and red numbers and lines are not easy to see, reconfigure the plot to make those darker or something.

L477 – It is 

L517 – seasons

L598 - cite the relevant reviews and syntheses here