Dear R1,

We thank both reviewers for their careful reading of our manuscript and for their valuable and constructive comments. We have revised the manuscript accordingly and believe that the changes have substantially improved its clarity and interpretation. Below, we summarize the main revisions made in response to Reviewer 1 (R1). Reviewer comments and questions are presented in italic, followed by our responses and the corresponding changes made to the manuscript.

Reviewer 1

We appreciate the reviewer’s comment regarding the use of DIC versus DOC in the Redfield ratio calculations: Particularly, the manuscript would benefit from an improved explanation why each C:N:P (total and dissolved, with DIC or DOC) is used.

The manuscript would benefit from a clearer explanation of the different stoichiometric ratios used throughout the analyses and the reason for their selection. The DOC:TN:TP ratio is described as the total (unfiltered) ratio, whereas the DIC:DIN:PO4 ratio represents the filtered fraction. However, DOC and DIC represent different C pools, affecting different ecological processes. When ecosystem metabolism is considered, DIC is particularly relevant for primary production, whereas DOC is more closely linked to bacterial production. I therefore encourage the authors to clearly define each ratio and explain why it is the most appropriate metric for addressing the respective aspect.

 In response, we expanded the explanation in the Methods section to better justify and distinguish the use of different carbon and nutrient pools (Line 175):

“DOC and DIC represent different carbon pools that affect different ecological processes. When ecosystem metabolism is considered, DIC is particularly relevant for PP because it is directly assimilated by photoautotrophs during photosynthesis. In contrast, DOC is generally unavailable to primary producers and is mostly utilized in heterotrophic metabolism, hence more closely linked to BP. The same goes for the dissolved inorganic nutrient pools versus total pools: the dissolved inorganic pool is directly available to phytoplankton (which could be autotrophic or heterotrophic), whereas the total nutrient pools include organic fractions, which would need (enzymatic) preprocessing, and which can have varying bioavailability (Berggren et al., 2025; Rulli et al., 2022, 2026; Soares et al., 2017). Both pools are therefore informative, but different. This is confirmed in our brown ponds; expressing the dissolved inorganic nutrient pools relative to DOC rather than DIC yields an average Redfield-normalized carbon value of 95 ± 11%, compared with 80 ± 16% (average ± SD) when normalized to DIC (Appendix Fig. 1).“

We also expanded the Results section (Line 223):

“Most importantly, browning increased the C:N and C:P ratios in the dissolved carbon and total nutrient pools, indicating lower TN and TP relative to DOC, while decreasing these ratios in the dissolved fractions, indicating lower DIC relative to DIN and PO₄³⁻ (Fig. 1A-B, D-E). This contrasting pattern suggests that browning enhances the availability of carbon substrates for heterotrophs while reducing the relative carbon resources available to photoautotrophs.”

Additionally, the manuscript would benefit from a careful revision to improve the consistency of abbreviations and chemical formulas. There is no clear patterns for elements and chemical compounds which are sometimes written as abbreviations and sometimes spelled out. I believe that this manuscript has the potential to make a valuable contribution to the field after the authors have addressed the comments raised below.

We harmonized abbreviations throughout the manuscript to improve consistency, and we carefully reviewed the entire manuscript, correcting typographical errors and minor inconsistencies.

Figure 1 could be improved to communicate the main message more effectively. I recommend adapting the color scheme to match that used in the mixed model (=changing from green to blue, also having in mind to use colorblind friendly palettes) to improve the consistency throughout the manuscript. Furthermore, the legend currently explains the ambient and warmed treatments, but the meaning of the color intensity is not described. Adding this information would make the figure easier to interpret.

We changed the color palette in Figure 1 as suggested. We agree that this substantially improves the figure and appreciate the recommendation. We also added information about treatments to figure’s caption.

Figure 2 would be presented more clearly by modifying the axis labels following the style of Andersen et al. (2025). In addition, I recommend including at least the boundaries of the depletion zones to panel B and C. This would help readers to identify more easily in which nutrient depletion zone the individual data points are located.

We carefully considered the suggestion to indicate the areas in panels B and C of Figure 2. We explored implementing this modification; however, it proved difficult to clearly define the areas, and because many data points overlap substantially, particularly in panel B, the figure becomes visually cluttered and more difficult to interpret. After testing several alternatives, we decided to retain the original version of the figure, which we believe provides the clearest presentation of the data. We hope the reviewers agree with this decision.

Line 168: It is not clear why DOC is included as a macronutrient for algal nutrient requirements, please clarify.

Please see comment above (Line 175).

Lines 185-187: Please explain more explicitly that increased DOM inputs (with DOC concentration as proxy) may also introduce DON and DOP as nutrients. Otherwise, this statement that higher DOC concentrations increase C:N and C:P ratios appears somewhat self-evident.

Thank you. We modified the paragraph (Line: 202):

“While increased cDOM and DOC concentrations increase the absolute amount of nutrients (open data), DOC strongly increased DOC:TN (Est. = 0.72, p < 0.001) and DOC:TP (Est. = 0.72, p < 0.001), indicating progressive carbon enrichment relative to N and P with browning (Fig 1A-B)”.

Lines 195-198: This sentence is very long and difficult to follow. Splitting it into two shorter sentences would improve readability.

We agree. We changed this sentence. Line 213.

Lines 201-203: I do not think this is the appropriate interpretation of the ternary diagram. An optimal stoichiometric ratio would be located near the 1/3 or each axis (Redfield ratio in the middle), rather than indicating, e.g. 0-15% of the algal P requirements. In my opinion, the manuscript already communicated the main finding clearly without this sentence.

We agree. We modified this paragraph substantially (Line 217).

“The ternary plots with Redfield normalized C:N:P ratios, confirm that ponds are consistently carbon‑rich, and therefore P and N- poor relative to Redfield proportions in both dissolved (DIC–DIN– PO₄^3-) and total (DOC–TN–TP) nutrient pools throughout the sampling season (Fig. 2B-C; Fig. S1). Most observations fell within the P-depleted and co N&P-depleted, and occasionally N-depleted regions of conceptual stoichiometric space (Fig. 2A). Stoichiometric imbalances were strongest in the dissolved fraction, which showed greater carbon dominance and more pronounced seasonal variability than total pools. Most importantly, browning increased the C:N and C:P ratios in the dissolved carbon and total nutrient pools, indicating lower TN and TP relative to DOC, while decreasing these ratios in the dissolved fractions, indicating lower DIC relative to DIN and PO₄³⁻ (Fig. 1A-B, D-E). This contrasting pattern suggests that browning enhances the availability of carbon substrates for heterotrophs while reducing the relative carbon resources available to photoautotrophs.”

Line 207: Please specify the saturation aspect in the context of C:N:P ratios. As currently written, "saturated" could be interpreted as referring to gas exchange equilibrium, which is not illustrated in the referenced figure).

We now call it “carbon-rich” or “enriched” throughout the text.

Line 208: Please specify what the reported optimum refers to.

We clarified the rationale behind the 1.2 cutoff value used in the manuscript by adding the following explanation (Line 230):

“The stoichiometric optimum that approximates the Redfield ratio (N:P = 16:1, molar) corresponds to a log₁₀-transformed value of 1.2 (10log (16:1)) for our molar concentrations (Figure 1).”

Line 217: Please add the unit to the value of 2.5.

The unit is now added. Thank you for noticing this.

Line 290 (Table 1):  For the row "log(TN:TP) - sampling time", the interpretation refers to "Strong seasonal control of TOC:TP", which I assume is a typo.

Line 290 (Table 1): In row log(DIC:PPO₄³⁻), there appears to be a typo (double P). In addition, the interpretation for sampling time states "no evidence", although the reported p-value is 0.04.

Thank you. We have corrected these typos. We also carefully reviewed Table 1 and implemented the suggested changes. We also standardized the wording and interpretation used in the "short interpretation" column to improve consistency across responses.

We again thank the reviewer(s) for their constructive comments and suggestions. We believe that the revisions have strengthened the manuscript and it is now ready for final publication.

Sincerely,

Aleksey Paltsev & Isolde Puts

I believe that the authors could provide a more detailed explanation of why shallow lakes are prone to strong and prolonged thermal stratification (lines 42–43), as this statement may not be clear to readers.

We agree. We substantially modified this paragraph (Line 41):

“Browning interacts strongly with warming. High cDOM and associated DOC concentrations frequently occur in warmer, lower‑latitude boreal regions, and the shallow morphology typical of boreal lakes makes them prone to strong and long thermal stratification (Houser, 2006; Pilla et al., 2018). Shallow lakes can experience strong and prolonged thermal stratification when high concentrations of dissolved organic matter increase light attenuation, causing heat to be absorbed near the surface, and disproportionally increasing surface water temperatures (Puts, Ask, Deininger, et al., 2023). This creates a stable density gradient that suppresses wind-driven mixing despite the lakes' shallow depth (Fee et al., 1996). The surface water (epilimnion) of stratified boreal lakes is mainly influenced by external inputs of elements from catchments. Hence in addition to disproportional warming, intensified and prolonged stratification during summer can increase cDOM and nutrient concentrations in surface waters (Bergström & Jansson, 2000; Puts et al., 2025), compounding the effects of browning on metabolic balance and resource availability especially in surface layers.”

Given that every ecological experiment has inherent limitations and cannot fully reproduce the natural conditions, I believe it would be worthwhile to add a paragraph to the Discussion addressing this issue. In particular, the authors could discuss the extent to which the experimental conditions may affect the robustness of the conclusions and the degree to which they can be extrapolated to natural lake systems.

We agree. We added this new section (3.5) to the manuscript (Line 366):

“As with the majority of ecosystem-scale experiments, our study simplifies natural shallow water systems. Although the EXEF ponds contain sediments, microbial communities, primary producers, consumers, and a natural shoreline, natural lakes have more variation in size and their catchments. Moreover, natural lakes have varying cDOM sources, with varying quality (Berggren et al., 2018). Thus, the experiment was designed to isolate the effects of browning and warming rather than replicate the full complexity of freshwater ecosystems. While DOC quality was constant across treatments (not seasons), natural lakes vary in cDOM composition, nutrient inputs, catchment influences, and mixing regimes, all of which can affect water physico-chemistry and productivity. Nevertheless, the observed patterns are consistent with large-scale studies of browning lakes. Our study does not catch the full spectrum of DOC concentrations found in lakes: the control lake had relatively high DOC values already, and thus pristine mountain lakes are not captured in this gradient. Nonetheless, because our conclusions are still based on responses across a broader DOC gradient, we expect the direction of the responses to be robust, although their magnitude may vary among lake types and climatic conditions. The unusually warm summer during the study may also have amplified temperature effects. Accordingly, our findings should be viewed as evidence for the mechanisms underlying browning-warming interactions rather than as quantitative predictions for all boreal lakes “

From a technical perspective, the manuscript would benefit from greater consistency in chemical nomenclature and the use of abbreviations. I also noticed several minor technical issues, for example, “DOC was and analyzed” (line 114), as well as a full stop at the end of the title in line 119. It would also be worthwhile to carefully check the syntax and grammar throughout the Methods section. 

Thank you for pointing this out. We checked the text and corrected typos and grammar. We also checked the abbreviations and “full text/their spelled versions”, and corrected them if necessary.

In Fig. 2, I would recommend adding the boundaries of the depletion zones to panels B and C, as this would make the figure easier to interpret.

We carefully considered the suggestion to indicate the areas in panels B and C of Figure 2. We explored implementing this modification; however, it proved difficult to clearly define the areas, and because many data points overlap substantially, particularly in panel B, the figure becomes visually cluttered and more difficult to interpret. After testing several alternatives, we decided to retain the original version of the figure, which we believe provides the clearest presentation of the data. We hope the reviewers agree with this decision.

We again thank the reviewers for their constructive comments and suggestions. We believe that the revisions have strengthened the manuscript and it is now ready for final publication.

Sincerely,

Aleksey Paltsev & Isolde Puts