We sincerely thank the reviewer for their thorough evaluation and the positive assessment of our study's scientific contribution, structure, and supporting data. We are particularly encouraged by their recognition of the integrated field-experimental approach and the conceptual framework.We fully acknowledge the reviewer's critical points regarding the need for substantial improvement in writing quality and the inconsistencies between the text and figures. We have taken these comments very seriously and have implemented comprehensive revisions to address them:

The entire manuscript has undergone extensive language polishing by a professional editing service by V. Monica Bricelj, Ph.D. from TechMar Resrch Inc. We have focused on improving sentence structure, clarity, terminology, and overall flow to enhance readability, while strictly preserving the scientific content.

We have carefully and systematically checked the entire manuscript against all figures and tables. All identified inconsistencies have been corrected. The text now accurately and precisely reflects the data presented in the figures.

We believe these revisions have significantly improved the clarity, accuracy, and professionalism of the manuscript. We are grateful for the reviewer's constructive suggestions, which have undoubtedly strengthened our paper.

All point-by-point responses to the specific comments are provided below.

Specific comments:

Line 24: Delete “an”.

Response: Thank you for pointing out this typographical error. The word “an” has been deleted from Line 24.

Line 27: Spelling correction needed for “significant”.

Response: Thank you for your careful reading. The spelling of “significant” on Line 27 has been corrected.

Line 37: The term “emission” is typically used for gases; consider alternatives such as “inputs” or “loading”.

Response: Thank you for this precise suggestion. As recommended, the term “emissions” has been changed to “inputs” in the revised manuscript (Line 37, now reads: “With the intensification of nitrogen (N) inputs and the control of phosphorus (P) emissions, P limitation has become widespread in global coastal waters (Zhang et al., 2024; Maavara et al., 2020; Liang et al., 2023) and has triggered adverse ecological consequences, including exacerbated eutrophication and shifts in phytoplankton community structure (Xin et al., 2019; Peñuelas and Sardans, 2022). ”).

Line 57: Please clarify “OP”; it likely refers to phosphate or dissolved inorganic phosphorus (DIP).

Response: Thank you for raising this point. The abbreviation “OP” did indeed refer to organophosphates. To avoid confusion, the text has been clarified as follows: “To cope with P limitation, microorganisms have evolved a range of strategies, including an increase in inorganic phosphate transporters, induction of hydrolases for scavenging organophosphates (OP, organic phosphorus compounds), and a reduction in P demand by replacing phospholipids with sulfur- or N-containing lipids (Van et al., 2006; Karl, 2014; Lin et al., 2016). ”.

Line 59: Replace “seas” with “coastal systems”.

Response: Thank you for the suggestion to improve the terminology. The word “seas” has been replaced with the more precise term “coastal systems” as recommended.

Line 66: This statement is repetitive; N:P limitation is equivalent to a high N:P ratio.

Response: We agree with the reviewer's point. The redundant phrasing has been revised for conciseness. The sentence now reads: “A high DIN:PO₄-P ratio (indicating N excess and P limitation) has been confirmed to be positively correlated with APA...” . This revision merges the two concepts into a single, clearer statement.

Line 68: Please clarify why freshwater inputs would enhance APA—does this relate to freshwater having intrinsically high N:P ratios?

Response: Thank you for this suggestion, which helped clarify the mechanism. As recommended, we have explicitly linked freshwater inputs to high N:P stoichiometry. The revised text now reads: “Freshwater inputs, which often carry nutrients with intrinsically high N:P ratios, can thereby enhance APA...” .

Line 87: Consider explicitly stating the objectives of the study at the end of the Introduction.

Response: Thank you for this constructive suggestion. As recommended, we have added a dedicated “Objectives of the study” paragraph at the end of the Introduction. It explicitly states our aims to identify the PO₄-P concentration threshold, evaluate the synergistic role of the DIN:PO₄-P ratio, assess seasonal and community-level APA partitioning, and validate these dynamics with genetic evidence, thereby refining the conceptual framework for AP regulation.

Line 92: Specify whether “mean depth” is intended. Also clarify the meaning of “half-exchange”.

Response: Thank you for these suggestions to improve clarity. We have revised the sentence as follows: “It covers an area of approximately 7,000 km² with a coastline of 320 km, a mean depth of less than 10 m, and a water half-exchange time (i.e., the time for 50% water renewal) of 55 days (Wu et al., 2023).”

Line 98: The phrase “affect the ecosystems” is vague; please provide region-specific examples.

Response: Thank you for the suggestion to make the ecological impact more concrete. The text has been revised to include specific, regionally-relevant examples. It now reads: “The resulting increase in N availability, coupled with intensifying P limitation, has triggered significant ecological shifts in the bay, including more frequent harmful algal blooms and changes in dominant phytoplankton species from diatoms to dinoflagellates (Song et al., 2017; Xin et al., 2019).”

Line 110: More detail on field sampling is needed, including sampling frequency and methods for water collection, transport, and preservation.

Response: The revision specifies that marine surface water was collected using a 5-L Niskin bottle. For riverine water samples collected at the mouths of ten major rivers, sampling was conducted following standard protocols for surface water monitoring in China (specifically, HJ 494-2009). An organic glass water sampler or a pre-cleaned polyethylene container was used to collect subsurface water at a depth of approximately 0.5 m. All samples (riverine and marine) underwent immediate on-site processing into aliquots for different analyses (nutrients, APA, molecular biology) to ensure comparability. It also clarifies that all samples were preserved according to the specific protocols detailed in sections 2.4.1–2.4.4 and transported on ice to the laboratory within 12 hours.

Line 121: Please justify the choice of an N:P ratio of 28 (half of 55). Clarify the rationale for the nitrogen and phosphorus concentrations used in the treatment groups, which appear substantially higher than in the control.

Response: Thank you for this suggestion to clarify the experimental design. We have revised the text to explicitly justify both aspects. The choice of the DIN:PO₄-P ratio of 28 for the treatment group (TG) was based on creating a clear contrast to the ambient ratio (55) and moving toward the classical Redfield stoichiometry (16:1) to test responses under mitigated imbalance. Furthermore, the higher absolute nutrient concentrations in the TG (DIN: 50.01, PO₄-P: 1.78 ) compared to the control (CG) (DIN: 1.90, PO₄-P: 0.04 ) were necessary to ensure that nutrients remained non-limiting throughout the 29-day incubation, allowing the target N:P ratio to be the primary variable influencing the system over time.

Line 123: Explain the rationale for sampling 17 times at 2-day intervals.

Response: Thank you for prompting us to clarify the sampling strategy. The sampling regimen (17 times over 29 days) was designed to capture the full temporal dynamics of the system. As detailed in the revised text, the frequency was actively adjusted: In parallel, culture water samples were collected 17 times over the 29-day incubation. The sampling regimen was actively adjusted based on observed system dynamics: a high frequency (approximately daily) was maintained during the initial period of rapid change. Once nutrients were largely depleted and biological activity plateaued, sampling intervals were lengthened to monitor the sustained response without unnecessary density.

Line 198: Given the dominant nutrient inputs from the Yellow and Xiaoqing Rivers (Fig. 2), analyses of N:P ratios for all rivers may be unnecessary, as the remaining tributaries likely contribute only a small fraction of total loading.

Response: Thank you for this comment. We agree that the Yellow and Xiaoqing Rivers are the dominant point sources. The comprehensive analysis of ten rivers, however, was conducted to evaluate the nutrient stoichiometry of the entire watershed. This approach confirms that elevated N:P ratios are a pervasive characteristic of the regional riverine inputs, not an artifact of the largest sources alone. This broader perspective strengthens the conclusion that anthropogenic nutrient imbalance is a basin-wide issue, which is relevant for managing non-point source pollution. The data have been retained in Fig. 2 to support this finding.

Line 216: Clarify how temperature and other environmental parameters were spatially interpolated.

Response: Thank you for this suggestion to improve methodological transparency. As requested, a sentence has been added to clarify the interpolation method (Line 216-218). The spatial distribution maps for all parameters (e.g., temperature, salinity, nutrients, APA, Chl a) were generated using ordinary kriging interpolation in Surfer (version 16, Golden Software LLC), a geostatistical method that accounts for spatial autocorrelation to produce optimal, unbiased estimates for continuous surfaces.

Lines 231–233: The N:P ratio results should be presented in the main text rather than in the supplementary material.

Response: Thank you for this suggestion. We agree that the DIN:PO₄-P ratio is a key parameter for interpreting the ecological status. In response, we have moved the relevant data from the supplementary material to the main text. The spatial distribution of the DIN:PO₄-P ratio is now included in Figure 3, alongside PO₄-P and Chl a, providing readers with a direct visual comparison of these critically linked variables. The corresponding description and discussion have been integrated into Sections 3.2.2.

Lines 261–265: The analysis described here does not appear consistent with the corresponding figure; please verify and revise.

Response: We thank the reviewer for their careful scrutiny. We have re-examined the correlation analysis and the corresponding Figure 4. The description in the original text was indeed not fully aligned with the figure. The relevant paragraph in Section 3.3 has been thoroughly revised to accurately reflect the patterns shown in Figure 4.

Line 273: Add subtitles to the figure indicating “summer” and “winter”.

Response: Thank you for this suggestion to improve the clarity of the figure. As recommended, subtitles clearly indicating “Autumn” and “Winter” have been added to the respective panels of Figure 4.

Lines 283–286: The text is not fully consistent with the figure content and should be revised.

Response: Thank you for highlighting this inconsistency. We have carefully revised the text in Lines 283–286 to ensure it accurately describes the nutrient dynamics presented in Figure 5. The updated description now clearly and correctly reflects the observed changes in DIN:PO₄-P uptake ratios, the temporal trends of the DIN:PO₄-P ratio in both the CG and TG, and the dynamics of DON and DOP concentrations during the initial phase of the enclosure experiment.

Line 310: APAtotal is referenced but not provided; please include this information.

Response: Thank you for pointing out this omission. As suggested, the average values for all APA components in the treatment group (TG), including APA_total, have now been explicitly provided in the revised text. The sentence now reads: “Average values of APA_phy, APA_bac, APA_free, and APA_total in the CG were 47.5, 22.6, 54.8, and 687.6 nmol·L^-1·h^-1.Average values of APA_phy, APA_bac, APA_free, and APA_total in the TG were 5.1, 2.9, 42.2, and 122.8 nmol·L^-1·h^-1.” This addition ensures that both the control and treatment group data are fully presented.

Lines 412–414: The proposed approach to reducing the N:P ratio by increasing phosphorus inputs may not be practical; please reconsider or further justify this recommendation.

Response: We agree with the reviewer that increasing phosphorus inputs to lower the N:P ratio would be counterproductive and impractical, as it could exacerbate eutrophication. Our intended recommendation was precisely the opposite: to emphasize source control of nitrogen to mitigate the N:P imbalance and restore ecological balance as the primary management lever. We have revised the text in the Discussion to clearly state that: Management strategies must prioritize the reduction of nitrogen inputs at their source to mitigate the N:P imbalance and restore ecological balance, rather than relying on intrinsic biological compensation within the coastal zone. We thank the reviewer for highlighting this ambiguity, which allowed us to clarify this critical point.