The manuscript by Rehder et al. Employs a process-based model for methane emissions from ponds to investigate who methane emissions from polygonal-tundra ponds will be affected by warming. This is a very important topic, especially now that we know that the Arctic has been warming faster than any other region in the world and that this warming may let to the proliferation of thaw ponds. Although the model seems to be robust, my major concern is the applicability of the model to other sites to be able to extrapolate the findings to other regions. Moreover, what about the representativity of the selected ponds regarding ponds in the Arctic?  In my opinion, a new section discussing how to upscale the results would be useful. Also, a sensitivity analyses of the models needs to be added.

Specific comments:

Abstract

Line 1  I suggest starting the abstract with the broad picture, i.e., mentioning that ponds are important sources of CH4 and vulnerable to warming. After that, authots can focus on the objective of your study.

Line 5  I think the abstract contain too many details about the model. That should be placed in the Methods section. Focus on the main characteristics of the model, its novelty, and the main results.

Line 9  Why these warming temperatures were chosen? Explain this later in the methods.

Line 10 Mention here that this increase in warming seems to be linear with temperature.

Introduction

Line 17            I have missed a first paragraph to contextualize the topic.

Lines 17-23     This paragraph contains some information that should be included in the methods or study site section.

Line 25            A quantification of the importance of ponds as a source of CH4 to the atmosphere needs to be included.

Line 50             Can not also young or recent accumulated C fuel methanogenesis?

Line 54            Add some information about how substrate quality affect CH4 emissions from ponds.

General           I would include a brief information about the model at the end of the introduction. Mentioning if there are other models that have been built, or why the MeEP is relevant and its novelty.     

Material and Methods

• MeEP seems to include vertical fluxes of water. What about lateral fluxes from the catchment? How would the model deal with those?
• Do the authors have some measurements of water temperature or other physic-chemical parameters to validate the assumption of well—mixed waters in summer? I ask this because I see that the model provides measurements every 1hours, while it takes half a day having a well-mixed pond.
• I suggested including a sensitivity test in this section. How having different types of vegetation would affect the results? I have been in areas where ponds are moss-dominated while in other areas from the same catchment, sedges were the most dominant type of vegetation. Also, what about porosity? That links with my previous question about how general or global are the results from the model.

Line 180:         there more studies in the area that show that these ponds are important sources of CH4?

Line 184:         What does “how compact the shape of the pond is” mean? (line 184)

Line 190          Please, justify why you assume NPP = GPP/2

Figure 3           The graph showns an R2 = 0.54, can the authors suggest with mechanismos could explain the rest of the variance?

Results and discussion

• Line 290. What about other processes not area controlled by depth? Groundwater connectivity, for example.
• Line 295. Is this result valid for all type of vegetation? Sedges vs mosses.
• Kuhn et al. 2018 – open water ponds, higher CH4 fluxes.
• Units: mmol m-2 d-1
• Line 305 Check Kuhn et al. 2008. Maybe authors need to be more specific and mentioning that these results are ponds from that specific area.

The manuscript by Rehder et al. focuses on the simulation of methane emissions from tundra ponds. The authors tackle an important topic given the unprecedented warming in this part of the world. Consequently, the abundance of such ponds could become even larger in the future. In order to simulate methane emissions the authors classified three types of ponds and applied a process-based model. The tuning of the model was achieved by using previously collected data in the Lena Delta - I thoroughly studied region in the Arctic. Furthermore the model is used to estimate methane emissions with ongoing warming.

The paper is well written and concise and the results are sound. Particularly the classification in different poond types as well as the contribution of different pathways and their subsequent attribution is intriguing. The major concern is the calibration of the model with this single site. I am aware that data, and particularly flux data from ponds are not widely available, however a detailed discussion on how different soil types or vegetation structure would affect the fluxes is necessary. The authors themselfes mention at the beginning of the manuscript (p4, l86) that this is a first order approximation for sandy and organic-rich sediments. Surely this is not the case for many other regions. There are some hints towards the upscaling of the results in the conclusion, however a distinct section on how the model can be used and particularly what is needed to achieve upscaling - more precisely what this would mean for the fluces at regional scale - would be very beneficial.

Two additional specific comments:

I was missing a clear research question and hypothesis

Figure 9: the combination of the area in panel b does not necessarily relate to panel a, Also in the caption you write about river terraces, yet in the figure nothing about these is mentioned

I hope these comments are useful and I enjoyed reading the manuscript.