Thank you very much for your valuable suggestions on this study, I have made the following changes to this paper as per your comments:

Comment 1: Lines 74-76. “In karst regions with low development, such as the karst areas in northern China, groundwater flow is predominantly laminar, largely complying with Darcy's law”. Insert supporting references for dominance of darcian flow in poorly karstified carbonate rocks in regions outside China:

- Agbotui P.Y., West L.J., Bottrell S.H. 2020. Characterisation of fractured carbonate aquifers using ambient borehole dilution tests. Journal of Hydrology, 589, 125191

- Medici G., Munn J.D., Parker B.L. 2024. Delineating aquitard characteristics within a Silurian dolostone

aquifer using high-density hydraulic head and fracture datasets. Hydrogeology Journal, 32(6), 1663-1691.

Answer 1: The above two supporting references have been inserted in the manuscript in line 74.

Comment 2: Line 117. Specify the 3 to 4 specific objectives of your research by using numbers (e.g., i, ii, and iii).

Answer 2: The specific objectives of this research have been specified in lines 118-123.

Comment 3: Lines 120-150. Insert information on the presence of faults that can either influence the groundwater flow, or represent preferential pathways for the recharge.

Answer 3: The information on the presence of faults has been inserted in lines 145-148.

Comment 4: Line 216. Specify that you are representing the advective flow velocities for the transport.

Answer 4: It was mentioned in lines 227-228.

Comment 5: Lines 487-642. Please, insert the two relevant papers on darcian flow in poorly karstified and fractured carbonates suggested above.

Answer 5: The two relevant papers have been inserted in the manuscript in line 74.

Comment 6: Lines 435-465. The objectives of your modelling research appear 4 by reading your conclusions. See my comment above in the introduction.

Answer 6: Three research objectives have been summarized and specified in lines 118-123.

Comment 7: Figure 1. I can see faults in your geological cross-section. They look normal faults. But, please explain this point in detail in study area section.

Answer 7: The information on the faults have been added in lines 145-148.

Comment 8: Figure 5a. Add the spatial scales. The vertical one cannot be detected.

Answer 8: The MAR wells, groundwater exploitation wells and groundwater level monitoring wells are all in the aquifers from the Majiagou Formation of the Ordovician to the Chaomidian Formation of the upper Cambrian. There are hydraulic connections of the aquifers and none of the wells are stratified.

Comment 9: Figure 6. Insert regression equations with the R2 values.

Answer 9: Regression equation and Pearson’s R have been inserted in figure 6.

Comment 10: Figure 9. Make the graphs larger and improve the graphical resolution of the figure.

Answer 10: Figure 9 has been improved.

Comment 11: Figure 11. Make letters and numbers larger.

Answer 11: Figure 11 has been improved.

Thank you very much for the valuable questions and suggestions you have raised regarding this paper. I would like to offer the following responses to your comments:

Comment 1: How do the authors quantify and address uncertainties in the improved two‐end‐member isotope mixing model, particularly given potential variations in isotopic signatures and possible contamination sources?

Answer 1: As you have pointed out, potential variations in isotopic signatures and possible contamination sources do indeed exist objectively. Firstly, our research group collected multiple rounds of isotopic samples from groundwater between 2021 and 2023, and the values of the two-end-member isotopes showed little variation, remaining consistent with the values mentioned in the paper. Furthermore, based on our preliminary investigations and research, we believe that the amount of water discharged from potential pollution sources is relatively small. While it might affect the nitrogen and sulfur isotopes of the groundwater, it is unlikely to have a significant impact on the hydrogen and oxygen stable isotopes. Regarding the issue you raised, we will add an explanation in the paper.

Comment 2: The study relies on an effective porosity value derived from tracer tests; how sensitive are the solute transport simulation results to variations in effective porosity and hydraulic conductivity assumptions, and how is this uncertainty evaluated?

Comment 3: What are the limitations of the groundwater flow model in capturing the spatial and temporal heterogeneities of the karst system, and how robust is the model calibration and validation against observed data?

Answer 2&3: Effective porosity and hydraulic conductivity are important factors that influence the results of solute transport simulations. In this paper, hydraulic conductivity is assigned to different zones in order to characterize the spatial heterogeneity of the karst system, and calibration has been performed using observational data. However, there is a lack of a quantitative description of the calibration results, and this will be addressed in future revisions soon. We did not subdivide effective porosity into zones but instead took the average value from tracer test results, which is a simplified approach. This decision was primarily based on the inherent uncertainty in hydraulic conductivity, one of the key inputs for calculating effective porosity. Moreover, subdividing effective porosity would lack a calibration basis. We acknowledge this limitation and will consider how to improve it in future work.

Comment 4: The analysis of infiltration efficiency uses empirical relationships (e.g., formulas (7) and (8)) to relate released water volume to actual recharge; under what conditions might these relationships fail, and how do variable hydrological conditions affect their applicability?

Answer 4: The empirical relationship between released water volume and actual recharge presented in this paper is derived from actual flow monitoring data. Therefore, when the released water volume exceeds the range of the monitoring data, this empirical relationship may no longer be applicable. This point will be further elaborated upon in the paper.

Comment 5: Considering the impact of MAR water quality on long-term groundwater sustainability, how do the authors define acceptable thresholds for contaminant levels, and what management strategies are proposed to mitigate the risk of groundwater quality deterioration over time?

Answer 5: The acceptable thresholds for contaminant levels in this paper are based on China's groundwater quality standards. Groundwater that does not meet the Class III water standard is generally considered unacceptable. In practical applications, however, this acceptable threshold may also be determined based on the requirements set by decision-makers, typically water resource management authorities, regarding groundwater quality.

Comment 6: I strongly recommend to cite below paper: "Assimilation of sentinel‐based leaf area index for modeling surface‐ground water interactions in irrigation districts"

Answer 6: The paper you mentioned conducts in-depth and meaningful research on the numerical model of surface water-groundwater interaction. We will reference it in the first chapter of our paper.

I sincerely appreciate your valuable suggestions for this study. I would like to provide the following responses to your comments:

Response to General Remarks:

As a representative region, the study area in this paper (the Baotu Spring Basin in Jinan City) reflects the general development characteristics of karst aquifers and groundwater flow patterns in northern China’s karst regions. Additionally, similar karst formations can be found in certain countries and regions in northern Europe. Therefore, the research findings and methods presented in this study may also be applicable to those areas. In response to your suggestion, we will incorporate relevant references in Chapter 1 and expand our discussion on this topic. Furthermore, we will add a discussion on the applicability of these research methods to similar studies.

Response to Detailed Remarks:

Your detailed remarks are very insightful, and we will optimize the figures and tables accordingly based on your suggestions. Additionally, we would like to provide the following clarifications:

1. Regarding Figure 2 and Figure 7: Figure 2 contains more information on wells and sampling sites compared to Figure 7. We will consider removing Figure 2 and merging its information into Figure 7.
2. Regarding Figure 5b: Since the recharge coefficient for rainfall infiltration is influenced by different land use types, its zonation does not completely align with the lithological zonation. We believe that Figure 5b remains necessary, but we will revise it to avoid redundant information with Figures 1a and 2.
3. Regarding the issue mentioned in Lines 444–448:

• First, we believe that the two research results are not contradictory. When the discharge exceeds 21.6 × 10⁴ m³/d, the infiltration recharge will be lower than the discharge; however, they remain positively correlated. Theoretically, the maximum recharge capacity of Yufu River can reach 114.9 × 10⁴ m³/d.
• Nevertheless, we acknowledge certain limitations in our study that may affect the accuracy of this result. For instance, during the flow monitoring period, the maximum flow in Yufu River was 36.72 × 10⁴ m³/d, which is still significantly lower than 114.9 × 10⁴ m³/d. This means that the linear relationship expressed in Equation (7) lacks sufficient empirical support when discharge exceeds 36.72 × 10⁴ m³/d.
• Additionally, this maximum recharge capacity was estimated under the assumption of a hydraulic gradient of 1. However, substantial recharge may lead to groundwater level rise, potentially invalidating this assumption. We will clarify these limitations in the paper.