This study presents a comprehensive dataset to characterize the rates and control of methane production across thermokarst lakes of different ages in interior Alaska. The authors conducted geochemical analyses and incubation experiments with sediment cores collected from a young (BTL) and an older (GSL) thermokarst lake. They observed elevated methane production rates at BTL, which was correlated with higher carbon lability for thermal induced reactions measured by Rock Eval analyses. They discussed how methane production varies with lake evolution and sediment depth, and also the influence of permafrost thawing on microbial activity. By comparing the depth-integrated methane production rates, they propose mechanism of how lake age and thawed talik thickness affect methane production rates and fluxes. The experiments were well-designed and the methods were generally sound. However, I have a few comments that need to be addressed before acceptance of the manuscript. 

Major Comments:

(1)    The stable isotopes of dissolved inorganic carbon in BTL were much more enriched in 13C than GSL, and the authors interpreted this as a result of methanogenesis. However, both methane concentrations and production rates were quite similar at two sites. So I wonder if methanogenesis could lead to such a large difference in 13C-DIC between two sites. Or if this could be related to the source of DIC. I also notice that both data of 13C-DIC and 13C-CO2 were present in Table S1, but I am not sure how were 13C-CO2 measured.  

(2)    Source of methane. The observed δ13CCH4 values from the incubation experiment were mostly >-60 ‰ particularly in BTL, with many of them >-50 ‰. This seems contrary to the biological production of methane with such positive δ13CCH4 values. Any explanation for this? Do you have a parallel killed control sample for incubations and how do they like? 

(3)    Following the above comment, it would be nice if the authors could include more discussion about the importance of different methane production pathways. 

(4)    Similar observations about the control of organic matter on methane production have been reported previously, which can be cited in this work. 

Zhuang et al. 2018. Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea. Geochim. Cosmochim. Acta 224: 171-186.

Maltby et al. 2016. Microbial methanogenesis in the sulfate-reducing zone of surface sediments traversing the Peruvian margin. Biogeosciences 13: 283-299. 

Berberich et al. 2020. Spatial variability of sediment methane production and methanogen communities within a eutrophic reservoir: Importance of organic matter source and quantity. Limnol. Oceanogr. 65: 1336-1358.

(5)    It is kind of confusing for the use of methane fluxes in Fig. 7. From my understanding, the production rates did not necessarily mean the emission flux from sediments to the water columns. I did not say the comparison was invalid, but please better justify it. 

(6)    Some figures such as Fig. S1 to Fig. S4 that contain important information should move to the main text rather than buried in the supplementary. 

Minor Comments:

Line 37: Remove the comma.

Lines 54, 317, 412: Revise and format the brackets.

Line 154: What was the purpose of the additional 3 mL sample? Please clarify.

Line 225: Should be "200 ℃".

Figure 2: Please indicate what A, B, C, and D represent in the legend. 

Lines 345 and 351: The term in situ should be used consistently and italicized throughout the text.

Figure 7: The figure is blurred and the resolution needs to be improved.

Lines 403–407: This sentence is vague and confusing. When you talk about significant difference, you need statistical analysis to support it. 

Figure 8: Please adjust the figure layout, as the overlapping text affects readability. 

Lines 485–491: The claimed correlations are not statistically analyzed. Please provide statistics and coefficients in the figure or text.