Thank you to the reviewers and Dr. Schourup-Kristensen for their constructive feedback, and to the authors for their thorough responses to the comments. Based on the reviewers' endorsements, I invite the authors to submit a revised version of the manuscript for further evaluation.

Dear Authors,

Thank you for submitting your revised manuscript. We have now received feedback from a third reviewer, who has provided constructive and detailed comments to further improve the manuscript. The reviewer’s suggestions primarily focus on expanding the model descriptions and clarifications, strengthening the model validation, and refining the discussion by removing less relevant content while elaborating on the key points.

Importantly, the reviewer observed that some concerns raised during the first round of review (though acknowledged in your response letter) were not fully addressed in the revised manuscript. Please ensure these points are incorporated in the current revision.

For your revision, please provide a point-by-point response that clearly connects each reviewer comment to the corresponding changes in the manuscript. Additionally, please explain how the revised text addresses each concern, specifying where modifications have been made.

We appreciate your efforts to address these comments and look forward to receiving your revision.

Best regards,
Liuqian

Dear Authors,

Please find the feedback from the reviewer. They acknowledged the improvements made in the revised manuscript but also pointed out that several important points still require further attention. Specifically, please ensure that all critical model components are briefly explained within the main text, followed by appropriate references to prior work, to make the manuscript self-contained. Additionally, please fully address the concerns regarding model validation, and refine the structure and content of the Discussion section according to the reviewer comments.

We look forward to receiving your final revision.

Best regards,
Liuqian

Please address the following minor comments before I can recommend acceptance for publication. All line numbers refer to the revised manuscript with tracked changes.

L3: For greater clarity, please specify the actual years this period represents.

L10: It would be helpful to include a brief comment on whether phosphorus retention (the 12% average) was found to be stable or also varied with changing riverine loads.

L15: Please specify under what conditions such achievement is unlikely. e.g., “...unlikely under the current management targets”?

L68: The phrasing "improve the input" is ambiguous in this context. Do you mean “... improve the representation of organic matter inputs from rivers in the model”? Please clarify.

L71: “a spatially high resolved…” -> “a high-spatial-resolution”

L87: “mode” -> “model”

L101: “light climate” -> “light field”?

L143: The single-sentence paragraph is redundant and can be deleted. The structure of the section is already logically implied by the subsection titles.

L145: “reasonable” -> “reasonably”

L145-155: Please cite the specific figures where the data (e.g., bottom oxygen, mass transport values, stratification) are presented.

L156: Please briefly specify the key variables assessed and provide a short summary of the overall conclusion from the model performance evaluation in the appendix. This will give readers context before they navigate to the supplementary material.

L160: Please provide the specific oxygen concentration thresholds used to define oxygen-depleted conditions and anoxia. e.g., < 2 mg/L or 1 mg/L?

L184-188: The statement that “a significant relationship between the retention rate and phosphorus loads does not exist” appears to be contradicted by Fig. 4b. The time series in Fig. 4b consistently shows higher relative P retention under the control run compared to the 50% load reduction, suggesting a load-dependent response. This conclusion is more accurately supported by Fig. 5d. The scatter plot in Fig. 5d shows no significant correlation when all data points are considered, which aligns with the stated lack of a significant relationship. Please clarify.

L187-188: Please provide the result of this t-test (e.g., p-value).

L190: Please provide statistical evidence to support the qualitative claim that the correlation for P “appears less pronounced” than for N in Fig. 6.

L193: Please clarify how the 40% and 12% retention estimates were derived. Are they the mean of the annual retention efficiencies calculated over the entire 25-year simulation period?

L193-194: As commented earlier, the conclusion that "the phosphorus retention capacity remains largely independent of load variations" is inconsistent with Fig. 4b. The argument should be based on the lack of a significant correlative relationship in the scattered data of Fig. 5d. Please clarify.

L246-247: Please cite the specific panel of the figure.

Figures 5-7: For the regression analysis presented in Figs. 5-7, please report the associated p-values to assess whether the correlations are statistically significant.

L257: Suggest rephrasing the subsection title as “4.1 Model performance and limitations”

L279-285: The statements in this paragraph should clearly distinguish between findings derived from the model and those from observations or literature.

L285: Please delete the citation of Fig. 1. Fig. 1 shows the location of Oder River but can’t see the high nutrient loads. Citing Fig. 1 is misleading here.

L290-291: The claim that the newly introduced limnic phytoplankton group was "necessary to achieve realistic biomass concentrations" requires substantiation. Please clarify: 1) where are the results for this group's abundance and its impact on biomass presented (e.g., which figure)? 2) what evidence supports the conclusion of "necessity"? Was this based on a model sensitivity experiment that compared simulations with and without this functional group? 3) please moderate the language to reflect the specific context of this study. Does this finding imply that this group is universally necessary for all model setups in this region, or was it a required component within the specific configuration of this model?

L292-293: The statement that the model can be applied in "coastal waters as well as in the open Baltic Sea" is somewhat vague. Please specify if "coastal waters" refers specifically to the Baltic Sea's coastal areas or to coastal waters in a global, general sense.

L294: Please express the spatial resolution in kilometers instead of nautical miles.

L300: The reference to Appendix A is too general. Please provide a brief summary regarding which aspects of model performance are analyzed in the appendix and state the overall conclusion of that evaluation to give the reader necessary context.

L305-312: Please clarify the methodological basis of the three cited studies. E.g., observational or modelling.

L310-311: Please cite the specific figure to support this statement.

L330: Please specify the exact panel (e.g., Fig. 5b) and report the corresponding correlation coefficient and p-value.

L337: Please specify the spatial resolution that is considered necessary (e.g., "on the order of 1 km or finer") to resolve the key coastal filter processes discussed in this study.

L357-359: The concluding statement that "For phosphorus, we did not find a similar dependence" on water residence time appears to be inconsistent with the visual data presented in Fig. 6b, which suggests a strong positive correlation. This claim cannot be definitively supported without a statistical test. Please clarify.

Dear Authors,

Thank you for submitting the final revisions. I am pleased to inform you that your paper is now accepted for publication in Biogeosciences.

Best regards,

Liuqian