This research demonstrated the impact that the TGD has the SW-GW interaction. Overall, the authors produced very interesting and valuable results. The manuscript was well written and the visualizations were designed well. I have a few minor comments below:

Line 30 - Abstract: Since the ZJ-JLX2 and HH1, HH2 is not previously described before the results – can you add in parenthesis a profile /geographic identifier (e.g. upper, lower, middle section below TGD, etc.).

Line 98 – Introduction – I recommend that you make a new paragraph for the SWAT-MODFLOW model and 1. Provide additional explanation about how and where its been used in previous research and 2. Explain and justify briefly how you will use it for this research.

Line 145: Rainfalland typo

Line 294-298: From Table 2 and 3 – It is not clear why you chose only 2 segments – the JLX1 seems like an anomaly in the segments based on Table 3– is there some justification why this is included in segment 1? I see your explanations in line 299-417 – but I’m specifically wondering why only 2 segments. Could you perhaps add a few sentences explaining this choice - or perhaps explaining the JLX1 anomaly?

Line 296: I think it would be clearer if you named the segments ZJ-JLX2 and HH1-HH2, especially since HH1-HH2 are explained this way in line 317.

Line 303-309 – These three features are the explanation for the segments – can you create a figure or visualization to show the hydraulic head groundwater drivers in each segment to justify this decision?

Section 4.3 – 4.4 – I thought the results provided here were very insightful and visualized well. The narrative was clear and you drew important connections and support from the literature.

This manuscript aims to investigate the effect of the Three Gorges Dam (TGD) on the groundwater cycle downstream. With that in mind, the authors examined the spatial extent of the Yangtze River’s influence on adjacent groundwater. The authors achieve this objective by leveraging monitoring wells and using a coupled SWAT-MODFLOW model to quantify period-specific surface water-groundwater exchanges. Additionally, the authors included a counterfactual scenario without TGD operations for comparison. The findings illustrate (1) the influence range of the Yangtze River on confined groundwater aquifers upstream and downstream, (2) the marked seasonality between the river and groundwater exchanges, and (3) the dampening effect of TGD in the overall interactions between the Yangtze River and groundwater.

I have read the manuscript with great interest. It is well-written, but needs minor revisions and clarifications. Below, I have listed comments, hoping they may help improve the manuscript’s quality.

Specific Comments

1. In lines 143-144, the authors state that the groundwater in the study area is primarily recharged by precipitation. Is this a result of the study, or something that has been determined in other studies? Do you have a citation?
   1. This reviewer understands the limitations of the current study. However, have the authors considered the potential role of Mountain Block Recharge (MBR) (Markovich et al., 2019; Wilson & Guan, 2004) in the study area? Have you considered collecting environmental tracers to determine the age of the water in the aquifers you are studying, and to assess the potential role of regional groundwater as a source for the confined aquifers?
2. It is not clear to this reviewer how the authors feed MODFLOW back into SWAT in their coupled framework. Did they use a drain boundary at the surface? What happens when the groundwater reaches the surface? Also, did the authors include a river package in the MODFLOW model that contains SWAT-derived information? I suggest including additional clarification on the model specifics to ensure interpretation and reproducibility.
3. The authors briefly mention a “wavelet coherence analysis” performed on the water levels (lines 406-409). However, the reviewer is unclear about how this analysis was performed in detail. Figure A5 is pixelated, and the conclusions drawn from this analysis are not clear from the figure. I encourage the authors to provide clarifications and citations in the methods section to ease the interpretation of these results.
4. I encourage the authors to include a paragraph discussing potential sources of uncertainty in their study, as well as its limitations and future work.

Technical Corrections

Besides the comments described above, I have a few technical recommendations for the manuscript.

1. This is a minor comment. In the abstract (lines 29 and 31), it is not clear what the ZJ-JLX2 section and HH1 and HH2 profiles are without reading the manuscript. I suggest including a descriptive term for the profiles (e.g., upstream or downstream sections) to aid interpretation from the outset.
2. In Figure 1, there are two cross-sections (1-1’ and 2-2’). However, these cross-sections are not shown in the figure until later in the text with Figure A4. I suggest referencing this earlier in the text (maybe in the paragraph starting in line 132), as it contains crucial geologic information that aids interpretation.
3. Correct “cclassification” in the Figure 2 caption for (d).
4. Change “SWAT-MODFLOW mode” to “SWAT-MODFLOW model” in line 421.
5. Correct “amd” in line 430.
6. In Table A1, the authors describe the Horizontal Hydraulic Conductivity as K_xy. This is misleading, as it makes me believe that the authors are using a different value for the off-diagonal elements of the hydraulic conductivity tensor. I suggest renaming this variable to K_x and K_y.

References

Markovich, K. H., Manning, A. H., Condon, L. E., & McIntosh, J. C. (2019). Mountain-Block Recharge: A Review of Current Understanding. Water Resources Research, 55(11), 8278–8304. https://doi.org/10.1029/2019WR025676

Wilson, J. L., & Guan, H. (2004). Mountain-Block Hydrology and Mountain-Front Recharge. In J. F. Hogan, F. M. Phillips, & B. R. Scanlon (Eds.), Groundwater Recharge in a Desert Environment: The Southwestern United States (pp. 113–137). American Geophysical Union. Retrieved from http://onlinelibrary.wiley.com/doi/10.1029/009WSA08/summary

The paper presents a combination of analysis and modeling approached to understand the impacts of the Three Gorges Dam at the hydrological and groundwater systems of the Yangtze river. I find the presented methodology interesting and well-fitting for the presented problem. The developed model can also be used as a starting point to evaluate different future management and climate scenarios for the river.

The paper is well written, illustrated with very nice figures. I found the number of abbreviations in the text sometimes a bit too much and confusing. I have a few comments and recommendations that in my opinion can improve the manuscript, I have listed them below.

General comments:

- I found the investigation period a bit too narrow. For the first data-driven analysis looking at a multiyear period would be neccessary to have reliable results to handle any short-term impacts.

- Could you provide some validation for the first approach? Also a few words about validating the non-TGD modeling results would be helpful.

- While I see the value in both approaches, I don't see how the two presented methodologies are connected with each other. Was the spatial influence analysis used in any way to inform or interpret the modeling?

Specific comments:

L27 - Please avoid using abbreviations in the abstract. These references to the specific sections are too specific for the abstract.

L63 - It is unclear which effects are you referring to here.

L159 - is there a reason for this specific, and relatively short time period? A reasoning for this should be provided.

L220 - For me the use of the letter K for this parameter is a bit problematic as it can be confused with the hydraulic conductivity which is normally signed as K in hydrogeology. I found this a bit confusing, but I understand if the authors just followed the terminology introduced in past papers.

At the same time I find this methodology really interesting and useful, and it is great to have it done before the actual modeling. I was wondering however, whether this is a completely separate step, or are the results of this step involved in some way to the SWAT+MODFLOW modeling?

Fig 3. - this is a very nice visualization! Is there a reason that the influence is only tested on the left side of the river?

L276 - does this mean that the relationship is dynamic over the year? It would be interesting if you could elaborate further, what is behind this dynamic. Also, extending the analysis to another year would be interesting to see whether the same periods behave similarly then (this could be a validation strategy).

Visualization on the changes of influence over the year would be also useful on the map.

L328: a reference and a short introduction of SWAT-CUP would be needed.

Fig4. - why is the peak in 2016/6 so better captured than the one in 2015/3?

L342: the groundwater level fits are much better then the discharge - why?

Fig 6. - is the dam location at the dashed line? (This is a very good discussion figure)

L388 - refer directly to fig6b

L389 - this sentence sounds weird, please simplify it

L416 - This section is really interesting. Would it be possible with your model to simulate different dam management scenarios too (in a future work)?