This is an interesting and data-rich research paper from a remote region of Chukotka, far eastern Russian Arctic. Here, the environmental history of Lake Rauchuagytgyn was reconstructed during the last 29 ka years, using ¹⁴C-dated sediment records of diatoms frustules together with organic carbon, nitrogen and mercury accumulation rates. Diatom assemblages responded to the major Pleistocene and Holocene environmental changes through shifts in species composition and abundance.  It appears that organic carbon in lake sediments has largely autochthonous origin, as it is strongly correlated with the diatom frustule accumulation rate. This implies that this type of arctic lake may play an important role as a carbon sink as most organic carbon (OC) is effectively buried in the sediments. However, OC concentrations in the sediments do not reflect the amount of carbon dioxide emitted during the ice melt, and this may be substantial.

I suggest that you change your discussion, conclusions and the abstract reflecting on existing uncertainty regarding the role of arctic lakes in the global carbon cycle.

The age-depth model of the long core, which was based on 23 ¹⁴C bulk organic carbon dates in a 651.75 cm core, was developed using LANDO modelling. This is in a broad agreement with the earlier published core chronology using different modelling and this gives extra confidence in the results. The short core was dated using ²¹⁰Pb and ¹³⁷Cs. The short core chronology is uncertain for the 7-11 cm interval.    

Overall, this is a valuable and thorough contribution to the series of recent publications from this remote arctic region, which may play an important role in the global climate change. It deserves a publication. Substantial uncertainty remains, however, regarding the fate of carbon in artic lakes and their role as sinks or emitters of carbon.

The manuscript is well written for the most part, although some of the sentences need clarifying or re-writing. I highlighted those in the attached pdf copy. In addition, there are several minor grammar mistakes which I corrected and highlighted in the attached pdf file.

Below I outlined sentences which need re-writing and other comments.

I suggest combining short and long core diatom and biochemistry data to facilitate visual interpretation of the results, please see the details below. This will also reduce the number of figures in this manuscript, which is quite high.  My other concern is the way sedimentation rates were calculated. It is not well described in Methods. I give the details below.

Abstract:

Line 37. Please change this sentence as uncertainty exists regarding the role of arcitic lakes in the global carbon cycle.

Methods.

Lines 195-205.

I suggest replacing the text with formulae and short justification of your calculations of sedimentation rates. You need to clearly describe how sedimentation rates were calculated to ensure the validity of the results.

Results.

Please combine Figures 5 and 6 into one indicating a gap between two cores. This would facilitate better visualization of the floristic changes.

Similarly, please combine Figures 8 and 9 into one figure, this would ease interpretation of the results.

Line 284. You refer here to Figure 5, not Figure 9.

Discussion.

Section 5.2.

Consider reviewing this section, it requires clarifying and re-writing. Use combined Figure made from Figures 8 and 9 to describe the changes and correlations between the profiles.

Lines 400-405. You need to re-write this passage about sediment accumulation rates, it is not entirely clear.

Line 407. This sentence about lake ontogeny (which is lake development) looks incomplete to me. You need to explain how lake ontogeny changes, this is a process.

Lines 409-410 – Similarly, it is difficult to understand these sentences. You need to think clearly what you are trying to say here, and re-write this passage. I highlighted it in the pdf copy.

Lines 462-465. These two sentences require reviewing and rewriting, it is not entirely clear what is the meaning there.

Figures.

Figure 10 is not easy to interpret, I do not think that this Figure is necessary, I suggest removing it.

It would be better to combine Figures 8 and 9. The combined Figure can be used to describe and discuss the trends in the profile changes and correlations between them.

If you wish to display the correlations, you can use a table.

Comments on the manuscript entitled 'Diatom responses and geochemical feedbacks to environmental changes at Lake Rauchuagytgyn (Far East Russian Arctic)' by Biskaborn et al.

This manuscript explores past environmental changes during the last 29k years based on diatom and geochemical records of a well-dated lake sediment core in Chukotka, which is a less investigated region. The results are interesting, particularly the relationships between diatom accumulation rates, organic carbon accumulation rates and mercury accumulation rates.  I have one major concern on the driving force on diatom flora shifts (see details as follows). I suggest that this manuscript can be acceptable after major revions. 

Major concern:

Although authors have provided potential driving forces for diatom flora shift, the mechanism is still ambiguous. The major trends in diatom flora are that an increase in benthic species during the early Holocene, and then the gradual replacement of benthic taxa by planktonic species. This general trend might be closely linked to temperature-driven changes in ice-cover period. For example, short ice-cover period in the early Holocene promote light penetration and the availability of littoral habitats.

In addition, effects of DOC on diatom flora should be considered during lake ontogeny since the deglaciation. DOC can be an important resilience against from external driving forces. 

Some references might be useful

Engstrom, D. R., et al. (2000). "Chemical and biological trends during lake evolution in recently deglaciated terrain." Nature 408(6809): 161-166.

Hu, Z., et al. (2018). "The Landscape–Atmosphere Continuum Determines Ecological Change in Alpine Lakes of SE Tibet." Ecosystems 21(5): 839-851.

Chen, X., et al. (2018). "Direct and indirect effects of Holocene climate variations on catchment and lake processes of a treeline lake, SW China." Palaeogeography, Palaeoclimatology, Palaeoecology 502: 119-129.

Wischnewski, J., et al. (2011). "Terrestrial and aquatic responses to climate change and human impact on the southeastern Tibetan Plateau during the past two centuries." Global Change Biology 17(11): 3376-3391.

I suggest that authors could clarify the major underlying driving forces of diatom flora shifts, specify the meanings of PC1 and PC2.

Other minor revisions:

1) L31-32: the responses to climate events are not very clear, probably due to low resolution of diatom records

2) L33-34: 'human-induced environmental change', please specify, atmospheric deposition?

3) L34-35:C/N ratios are generally larger than 10 during the Holocene, suggestive of the mixture of within lake production and terrestrial organic matter. Therefore, it should be cautious to draw this conclusion.

4) Section 2 Study site: Please provide more details on aquatic plants in this lake. Are there macrophytes or mosses around the lake shore? This is important to explain the development of benthic diatoms during the Holocene. In addition, water chemistry data should be provided, such as pH, conductivity, and dissolved organic carbon,

5) Section 3.5 Data processing and statistics: L 173, generally,  square-root transformation of percentage data were used in CONISS, please check. In addition, the number of zones should be tested by the broken stick model (Bennett, 1996).

Bennett, K. D. (1996). "Determination of the number of zones in a biostratigraphical sequence." New Phytologist 132(1): 155-170.

6) L243-246, please check the units of DVC and DAR,  superscript should be used.

7) L330-331:  thick ice due to long ice-cover period probably reduces light penetration?

8) L339-340: more detailed explanation for the linkage between diatom flora shift and climate. During this stage, the major change is the disappearance of Linvidavia bodanica and L. cyclopuncta

9) L354-355: rising alkalinity might be linked to enhanced chemical weathering intensity of bare rocks under warmer and wetter climate during the early and mid-Holocene

10) L371: the influx of melted water during the spring and summer probably increase the mixing?

11) L396: Here, potential effects of nitrogen deposition?

12) L488-489: prolonged ice-free period increases the availability of littoral habitats

13) Figure 7: legends for the two figures are needed, depths can be changed to 'ages'

14) Figure 8: for the total percentage of light Lindavia, L. bodanica might be different from other species, since this taxon has relatively heavy valves, which are similar to some Aulacoseira species (see the review by Saros and Anderson, 2015, The ecology of the planktonic diatom Cyclotella and its implications for global environmental change studies).