Dear Authors,

I have very much enjoyed reading your work. The contribution which looks back on what material we actually analyse, and on what are the inherent sample limitations is valuable and timely, in particularly now, when technological advances allow for more precise and more sophisticated measurements. The paper is informative and generally well written, and Biogeosciences is a most adequate venue for this work.

I have several general minor-to-moderate comments which (I hope) will improve the readability and the reception of the manuscript.

The language – please try to be as specific and consistent as possible. Dealing with isotopes and environmental controls, the vocabulary can be daunting, especially for less familiar readers. Please, when talking about ‘precipitation’ note each time if you refer to atmospheric (rainfall) or carbonate precipitation. Also, perhaps it is worth to explain once and upfront (but not as in the present version in the abstract) all the environmental factors influencing isotopic composition of carbonates and their direction. As of yet, provided explanation is correct but condensed to two long and complex sentences in the abstract. Again, please keep in mind readers less familiar with principles of stable isotope geochemistry and shrieking when ‘fractionation’ is mentioned. The fact that oxygen isotope fractionation is temperature-dependant, but the process happens (1) in the atmosphere and (2) in the ambient water, and drives the isotopic composition of water/ carbonate in two different directions is probably best explained using a simple sketch? I do agree that a picture is worth a thousand words, and in this case a well-designed but simple figure could improve the clarification of processes influencing d18O in lacustrine carbonates. Such figure would be a great asset in the introduction. Shall you decide to leave out the sketch option, please explain the processes consequently starting with atmospheric temperature effect on rainfall oxygen composition and lake water composition (additionally through evaporation) and only then move to ambient water temperature influence on carbonate precipitation (modified by vital offsets).

In the chapter ‘Material and methods’ the ‘material’ is actually not described. An SEM image of Candona, an SEM or macro image of Chara elements and perhaps a macro image of Pisidium would be a good addition. Also, I would welcome a sketch of Chara components (branchlet and internote) as I am familiar mostly with oospores and it took me a while to understand what to you refer to as ‘encrustation’.

Field sampling. I wish to see a more detailed information on field sampling. How do one take a less than 1 cm surface sediment (with a small shovel) from a water depth of more than 1 m? I imagine that one needs to employ a diver? How was the water sampling in 2013 and 2014 done? With Niskin Bottles? How was the Chara sampled? I see no justification for sampling Lake Blaktjärnen – its Chara results are not well incorporated into the rest of the paper. Please, if you want to keep them make sure that the reader knows why they are relevant and how they fit into the general picture.

I feel awkward promoting my own work, but you may want to refer to the papers by McCormack et al., 2018 and McCormack & Kwiecien 2021; the most recent component-specific studies of lacustrine carbonates. While Lake Van setting and chemistry are very different from the lakes you are working with, these papers highlight the suboptimal suitability of bulk carbonate samples for paleoenvironmental reconstruction and elucidate which factors can compromise the bulk signal.

I really like that the conclusions loop back to the relevant goals listed in the introduction. Having said that I find the conclusion misleadingly presented. I agree that differences in vital offset -corrected d18O values of different carbonate components suggest different periods of formation and might point to the amplitude of seasonal temperature contrasts. This holds true only if several components are extracted from the same sedimentary layer and their isotopic composition is compared and contrasted (conclusion 1). However, this information is interwoven with influences of lake water d18O and temperature. By the time the reader reaches conclusion 2, the essential notion of comparison is already forgotten, and it reads like any seasonal change in water temperature is clearly reflected in d18O of any biogenic carbonate, and I cannot agree with this statement. The order of arguments provided in conclusion 2 does not strengthen it either. Please, streamline the arguments towards the conclusion, not away from it. Again, a well-designed sketch in the introduction, could help in making this conclusion more succinct. Conclusion 3, while correct, is very loosely formulated and, in its present form reiterates the findings of McCormack & Kwiecien 2021. Your work deals with a more complex example and is the first such comprehensive attempt of comparing carbonate components from shallow water, above the thermocline of an open lake (as explained in conclusion 2). I think that focusing conclusions on this particular case and making them more specific will be very beneficial.

Specific comments:

Abstract

Line 4: 'lake water and water temperature'

Lines 21-25: this info is correct but as a 'textbook knowledge' is unsuitable for the abstract

Introduction

Line 36: 'depending on the local context'

Line 40: remains of lacustrine organisms

Lines 40-45: open lakes are more prone to calcite than aragonite precipitation, but carbonate mineralogy also plays a role in bulk carbonate d18O composition. Please, check McCormack et al., 2018

Line 76: their - whose?

Material and methods

Line 177-178: were the valves visually checked for organic matter remains? Was the potential organic matter left intact?

Line 184-185: valves? I was under impression that gastropods have shells and operculum but not valves

Results

Lines 235-239: this is interpretation, not result

Line 268: 'surface sediment' is misleading if it refers only to encrustations collected from the surface but not to the bulk surface sediment

Lines 267-275: information provided here is correct, but it is not a result

Line 286: and what about autochthonous carbonates? Can you exclude/ discuss their presence?

Lines 308-313: information provided here is correct, but it is not a result

Lines 326-329: information provided here is correct, but it is not a result

Line 326: exobiotic mentioned for the first time without explanation

Discussion

Lines 344-346: correct information but should be better explained in the introduction (see general comments)

Lines 449-453: without clear reference to a figure, I cannot see how your results demonstrate these two points. Also, the points are very vague - what do you mean by 'sufficiently large'? How do you know or how can you test what is an 'representative average'? Please, try to rethink this argument.

Figures

All figures are informative but with small adjustment they could convey the message more efficiently.

Fig. 2: Please, indicate clearly 8 m water depth mark (the deepest sampling point). If the grid is necessary in the figures, please, align the legend within the grid boxes. Also, please put the data points in the foreground not in the background. The present effect is visually unsettling.

Fig. 3: Please, align the legend within the grid boxes. I am not sure if the symbols in the upper left and right corner of figure 3a are intended?

Fig. 4: Please, make the data points in panel 4a larger, they are barely visible. Similarly, the triangles in panel 4b

Fig. 5: Please, unify the scales in fig a and b (panel b is visibly horizontally stretched, although the range of the values is the same) also the ticks on the d13C axis are suboptimally distributed, if taking the grid into consideration (with the grid values at -10, -8.75, -7.5 and so on).

Fig. 6: Please unify the scales in fig a and b (panel b is visibly horizontally stretched although the range of the values is the same). The legend is a bit confusing; it took me a while to figure out what am I looking at. ‘Sediment sample’ even if explained in the legend is misleading, why not calling it ‘dead fragments' or 'subfossil fragments'?

Fig. 7: The grid is distracting. If the authors want to keep the grid why not stopping at full intervals (e.g.: -7.5, -2.5 for d13C and -8, -4 for d18O) rather than cutting it of randomly?

Fig. 8: What are exactely 'dead' and 'living' samples? Are the fragments of encrustation described as 'sediment sample’ in the legend of figure 6 considered 'dead'? Please, define the term and use it consistently.

Fig. 9: The same comment as above about the grid

Table 1: The species, instar and the no. samples are the same for both panels, I suggest merging them into one. For the consistency, I would suggest adding all data presented in figure 7 (including 'fine calcite', 'fragmented encrustation from surface sediments' and Chara samples from Lake Blaktjärnen). Please, also indicate if these are measured or vital offset -corrected data. Last comment here - please try to keep the terminology consistent throughout the main text, figures and figure captions and the table.

To wrap up, I think this is a really valuable contribution showing pitfalls of using single carbonate component and highlighting the interpretational difficulties but, also benefits of multi-component analyses, and I very much wish to see it published. I hope that authors will find my feedback helpful.

Best wishes, Ola Kwiecien

The study by Labuhn et al. discusses an interesting issue of applicability of oxygen stable isotope measurements in specific lacustrine carbonates in reconstructions of past water temperatures. The study adds to the already existing knowledge as pointed out by authors.

I found the manuscript well written and interesting. The introduction is informative and points out the key information based on the available literature sources. The data are well presented with high-quality graphics. The authors discuss the possible mechanisms that control the stable isotope composition of the carbonates studied and explain the possible reasons for the differences in the stable isotope composition of encrustations and shells.

The study confirms the established knowledge that due to the differences in stable isotope composition δ¹⁸O measurements should be performed on the specific types of carbonates instead of bulk carbonate samples of unknown and potentially time-variable composition. The most important outcome of the study is showing that by studying selected carbonates it is possible to estimate seasonal water temperature changes.

Despite the overall good quality of the study I suggest considering the specific comments listed below before the manuscript can be accepted for publication.

Specific comments:

Line 4: change ‘on’ to ‘by’

Line 98: delete double ‘the’

Lines 145-148: I would not limit the growth of Chara to May-July. What about August and possibly also September? You suggest that charophytes studied are perennial.

Lines 156-157: What was the bottom area (cm2) where each of the surface sediment was sampled?

160-162: Information about the sampling of charophytes is lacking. Were the whole macroalgae taken? Cut at the water-surface sediment interface? How many individuals of each species were sampled?

Lines 168-169: Since I was involved in the studies of the isotopic composition of recent charophytes I have also tried to remove organics with H2O2. I have never managed to remove all. Part of the stem was always resilient and remained after the treatment.

Line 169: Please explain what the ‘fine-grained calcite sticking to the encrustations’ is. Why did you remove it? How do you know that you did not remove a fraction of encrustations at the same time?

Lines 255-257: I guess both living specimens and Pisidium shells taken from surface sediments in fact originate from the surface sediments therefore it is better to say: shells of living Pisidium specimens and empty Pisidium shells

Line 257: probably it would be good to change ‘living and dead samples’ to ‘shells of living and dead mussels’

Lines 263-264 and 380-382: Charophytes – you studied ‘single stalks from an internode or branchlet’. Encrustations at one specimen are not formed at the same time but as charophytes grow. Therefore in the isotopic studies of charophytes, specific fragments were studied, e.g. apical fragments. The variation of stable isotope values of charophyte encrustations studied may result from the fact that different fragments had CaCO3 precipitated at slightly different times, i.e. as the charophyte grew. In my opinion, the larger isotopic range of Chara hispida is also due to the gradual seasonal growth and precipitation of encrustations in the changing ambient conditions.

Lines 264-265: Do you have confirmation that Chara hispida from the lake studied overwintered? Charophytes are not always perennial. Overwintering can occur but it is not a rule. I have observed this during the field studies I participated in. You can have a look at publications e.g. of Mariusz Pełechaty – an experienced charophyte scientist with extensive field experience, in which the issue is discussed.

Lines 265-266: Whole new and several dozen cm high charophyte can grow within one season –personal field observations.

Line 266: Which internodes and branchlets were sampled? Apical ones or fragments from different parts of charophytes. Also, what were the sizes of charophytes? How tall were the macroalgae studied? This information is important in the context of the discussion. Thick and dense charophyte stands can form a specific microhabitat, they can also limit the extent of water mixing to the bottom.

Lines 279-282: This difference may result from the intensity of photosynthesis and density of charophyte patches.

Lines 283-284: Here ‘fine calcite’ is mentioned once again, what kind of calcite is that? More explanation is needed.

Lines 317-319: Influence of stratification is mentioned here however, previously in the manuscript it was stated what waters within the epilimnion are well mixed and looking at the data one can see that thermocline is below the deepest site sampled. Also, see lines 345-348 and most important lines 352-357: These fragments confirm my concern about interpreting δ¹⁸O values in Candona as related to water stratification.

Lines 324-329: Also, δ¹³C of adult ostracods is lowest because of water mixing and return of the ¹³C-depleted DIC of the waters from below the thermocline

Lines 424-425: Which is an apparent drawback.

437-438: Temperatures absolutely unlikely to occur. In central Europe, even during days with temperatures > 30 during the day, water temperature in the epilimnion reaches 24-25oC.

Fig. 3a: Why don’t you present the complete, i.e. whole year precipitation and temperature data for the year of sampling – 2018? This may differ from the long term data. In fact, the difference is already visible, especially in precipitation values.

Sincerely,

Karina Apolinarska