The article considers an extremely important phenomenon – the entry of methane into the water mass of the Arctic river from its catchment area. It is shown that methane is distributed inhomogeneously in the transverse direction, its highest content is characteristic of coastal areas. This work opens up the direction of research necessary to assess the flow of methane into the coastal zone of water bodies during the melting of permafrost. A large number of studied indicators gives grounds to confirm the results obtained. The conclusion seems to be important that a considered fraction of CH4 is already oxidized within the recently thawed active layer.

From the comments on the work, the following should be mentioned. Dissolved organic carbon is among the studied indicators. Why do the authors use this indicator, and not the total organic carbon, which seems more correct, since organic suspension can be a carbon source for methanogens? The second remark concerns the authors' conclusion that the upstream river sections are not a source of CH4 entering the Arctic Ocean by transferring downstream with river runoff. It is possible that this is the case in low-water phases, and during the period of maximum flood flow, the time of water reaching can be significantly reduced. The study of the length of the river section from which methane enters the mouth in various phases of the water regime was not included in the list of research tasks, but this idea seems very relevant for further work. Another remark concerns the reference to Figure 7. The authors write: statistically significant correlation between methanogen abundance and methane concentration (Fig. 7). Figure 7 in the appendix shows other data.

Despite the above comments, the work seems to be very important and should certainly be published.

Summary of the paper: The highest methane concentrations in an Arctic river are linked to local terrestrial inputs. Castro-Morales et al. studied methane concentrations on a 120 km portion of the Kolyma River during the late freshet (twice in June 2019). They observed a strong spatial disparity along the river bed with higher concentrations linked to warmer temperature, low conductivity and closeness to the river bank. This high spatial resolution study in the Kolyma River is the key start to better understand methane concentration pattern in (Arctic) rivers and their potential as methane source/sink. The correlation with temperature is interesting as it poses the question of increasing methane emission from Arctic rivers during the current global warming. It would be great to confirm if the microbes detected during this study are alive (active in the river itself) or dead (originating from the nearby permafrost surficial soils as stated by the authors) by sequencing RNA, although this type of sampling comes with logistical challenges in such remote environments. Overall this study is well done and brings key findings.

Main comments:

• Why did the authors choose to only study dissolved organic carbon (DOC) as a food source of their methanogens while particulate organic carbon (POC) could a food source as well? Especially because the GF/F filter used to filter the water for DOC could be used to quantify POC. Eventually, DOC concentrations are not used at all in this study and could be removed.
• Were there any new OTU detected during the study? If so they should be deposited in GenBank.

Minor comments:

L364, 369: Could you add the instrumental error on the measurement of pCH₄?

L437: Was the river anoxic where Methanobacterium, and Methanoregula were detected? If not, are they rather active or dead (originating from the nearby terrestrial environment)? Did you consider methane production within the river as this as been detected in other aquatic environments (see Bogard et al., 2014 (Oxic water column methanogenesis as a major component of aquatic CH4 fluxes, Nature).

L457: r² = 0.11 and 0.21 are rather low correlation coefficients, can you add p values? If p is not significant this needs to be indicated so as to not mislead the reader on the presence of correlation.

L459-470: The paragraph on DOC concentration comes a bit out of the blue after the microbial analysis, maybe add its separate paragraph? Especially because it is not used afterwards

L585: Some methanogens have been detected in oxic environments before, see Bogard et al., 2014 (Oxic water column methanogenesis as a major component of aquatic CH4 fluxes, Nature).

Typographical corrections:

Since you choose to simplify methane as ”CH₄” please to do homogenously in the manuscript