Llodra-llabres et al conducted a paleoenvironmental study of an alpine lake in the Sierra Nevada Mountains of Spain. They focused on using algal pigment concentrations and pigment composition to evaluate changes in the algal community in through time, attempting to link changes to climatic changes and atmospheric deposition. I think this effort has merits and could become an excellent paper, but as it stands needs major revisions.

General comments

• In general, the manuscript could use a stronger narrative, more cohesive arguments and clearer focus. At present, the study reads like an exploratory or “fishing” exercise: many variables are measured, compared broadly, and interpreted post hoc. This approach makes it difficult to build a clear, mechanistic story and does not lend itself to a cohesive narrative.

All of the key elements are present and the dataset is interesting, but the analyses need to be more directed. Specifically, hypotheses should be clearly articulated and explicitly linked to the data and figures. For example, if the authors propose that nitrogen deposition is not important but dust inputs are, they should present proxies for both alongside the relevant pigments in the same figure and directly evaluate those relationships. The likely mechanisms should also be clearly described. Paleo data inevitably limit causal inference, but plausible mechanistic links supported by statistics can still be developed.

• The manuscript also includes an excessive number of figures that do not highlight the key take-home results. The main text should be limited to ~4–5 figures, each telling a clear and focused story aligned with the primary conclusions. Currently, many plots present time on both axes or show variables independently, making it difficult or impossible to visually evaluate the relationships being claimed.
• Greater care is needed when drawing conclusions from correlations. For example, showing a statistical relationship between pigment PCA results and a climate metric does not demonstrate that dust is driving pigment changes. The manuscript does not clearly articulate the mechanisms behind these relationships, instead relying heavily on literature examples. While prior work provides context, it cannot substitute for evidence within this dataset. Similarly, C/N ratios are not exclusive indicators of algal versus terrestrial material. Interpreting them this way, particularly in a lake above treeline, is questionable. These types of interpretations suggest insufficient consideration of what each proxy truly represents, its limitations, and the mechanisms that could explain observed changes.
• The discussion section is also unfocused, reads largely as a literature review, and is overly long. It should instead concentrate on interpreting the results of this study specifically.
• In addition to the issues with the narrative and presentation, I think more explicit data could be used to link the algal proxies to deposition. If you are not going to use proxies of either yin your own sediment record (which would be best). You could at least temporally compare them to your data; there are well constrained records of both dust and N deposition in this region, why not explicitly use those in your statistical evaluations and data presentation.

Detailed comments.

1. Consider quantifying the “richness” of nutrients in dust by comparing them to local bedrock and calculating enrichment factors. Saharan dust is generally low in organic matter and phosphorus, and phosphorus is often mineral-bound and slow to become bioavailable. Also, “rich in alkalinity” is imprecise; consider rephrasing as “rich in alkalizing minerals” or “minerals that increase acid-neutralizing capacity.”

Em dashes seem to be a mark of AI writing these days aren’t normally used so frequently in standard text. This is just my personal opinion, but they should be restricted to when you really need to highlight something. I would remove them.

174 – High C/N ratios can also reflect nitrogen limitation and/or diagenesis, both of which may be more plausible interpretations given that the lake is above treeline.

Results

Can you show the Chlorophyll-a to Pheophytin-a ratio, this will assist with interpreting degradation. I know some of these pigments are more or less susceptible to degradation, like diatoxanthin.

Also, I know its common to plot pigmetns etc by relative abundance with similar sized x axis, but it makes it hard to see the temporal changes in indicator pigments where the concentrations are less than 10%.

Can you plot your explanatory variables along side your data? You have a mix of graphs with time on the y or x axis, which makes it difficult to evaluate temporal relationships. Pick one way of showing the data, and stick to it.  There is a lot of figure space given to PCA plots and plots that are repetitions (d15N vs Aphanizophyll (repeated from fig 3), but I would rather see more interpretable graphs,  e.g. showing temporal changes in proxies alongside the predictor variables as well as predictor plots.

You should use statistics to evaluate whether or not you are observing significant changes in your proxies through time.

Why is the C/N ratio being compared to climate and atmospheric variables, what are you specifically testing here?  

Regarding dust, I did not see Zr/Al or similar elemental proxies presented. Were these measured, or are you relying on external studies to make these links for you? It is important to show how dust inputs are linked to your dataset. Plotting dust indices (e.g., wNAO, SPI) directly alongside pigment proxies would help establish clearer connections between drought, dust production, and specific pigment responses. Or better yet, find other clear data streams showing the relevant data. I’m not saying these relationships don’t exist in the real world or even in your data, I’m just saying that they way you have presented the data is very cursory and does not make it clear.

Line 415, did you explicitly show markers of increased dust deposition in your lake or is this entirely based off of other publications from nearby lakes? You haven’t not made this relationship clear or explicit.

Why are you comparing your results to examples of lakes below treeline?

The discussion should be written as to highlight your main take home messages. What have we learned from your study, specifically? It is ok to compare and contrast to other studies, but this discussion opens paragraphs with other publications, more like a literature review, and is consequently excessively long.

Personal opinion, but the titles of the subheadings are a bit long

439 How are you defining ‘alpine’, alpine is above treeline. Not all these publications are for lakes in the alpine. Mountain does not equal alpine. Please also be precise with citations.

645 would you expect very colored DOC at this elevation though? … a few lines later you mention a bog. Is this in the catchment? What vegetation is in the bog? You probably should include that in the site description!