I have read the manuscript and carefully considered the comments provided by the two reviewers. Both reviewers recognize the relevance and potential value of evaluating Causal Discovery (CD) methods against traditional correlation-based approaches in complex hydrometeorological systems. However, they also raised several substantial concerns regarding methodological choices, the physical interpretation of causal structures, and the robustness of the time-series prediction evaluations.
Regarding the restriction to one-day lagged causal effects raised by the 2nd reviewer, I have read your rebuttal, but I agree with the reviewer that this remains a significant concern.

While I understand your argument, the physical variables being simulated, such as soil moisture, snowpack, and groundwater, inherently possess long-term memory in the real world. Limiting the benchmark strictly to a lag-1 relationship may fail to thoroughly test the methods' ability to handle the multi-step dependencies they will inevitably encounter. To adequately address this point, please implement one of the following approaches: either include a robustness check or sensitivity test, or provide a substantially stronger justification. You need to provide a compelling theoretical justification for why a lag-1 restricted evaluation remains a fair, robust, and comprehensive benchmark.

Generally, please revise your manuscript accordingly and submit a marked-up version of the text highlighting the changes made, along with a detailed point-by-point response to the reviewers' comments. Ensure that all newly introduced figures and tables in your response document are labeled distinctly (e.g., Table R1, Figure R1, not Table 1, Figure 1) so they are not confused with the manuscript’s main text Tables and Figures.

Dear Authors,
As the Editor, I have also carefully read through the manuscript to provide a final check and have noted several minor editorial and grammatical details that need to be addressed before we can proceed with official publication.
Please revise your manuscript according to the following itemized points:
1. Grammar and Punctuation (Comma Splices) Throughout the manuscript, there are several instances of "comma splices", where two independent clauses are improperly joined by a comma instead of a period, semicolon, or conjunction. Please carefully read the entire manuscript to correct these. Some specific examples include:
• Lines 149–150 in the track changed version (also for the following line numbers): The sentence discussing "establishing causality..." appears to improperly join two separate thoughts. Please split this into two distinct sentences.
• Line 165: "We also compare our results with a non-causal method, we conducted the analysis..." Please separate these into two sentences or use a semicolon.
• Lines 272, and 275: Similar comma splice issues occur here (e.g., “TCDF can be divided into two broad steps, the first step involves identifying the potential causes of each variable by training deep neural networks.”, "The first step forms the major analysis of TCDF, it can be broadly divided...").
• Figure 2 Caption: "We extracted data from locations... , these locations are spread across 5 river major river basins." This should be broken into two sentences. In addtion, the “river” after 5 should be removed.
2. Scientific Clarification (Line 243) Regarding the sentence: "The vertical distribution of soil profile is derived from relations explained in Clapp and Hornberger (1978)." Please revise this for scientific precision. The Clapp and Hornberger (1978) model primarily provides soil hydraulic parameters, which typically need to be incorporated into a framework (such as the Richards equation) to calculate the actual soil moisture distribution. The current phrasing ambiguously implies that the 1978 model provides the soil moisture directly. Please clarify this wording to avoid confusing the readers.
3. Formatting of Section Headings (3.4.1 to 3.4.4) Please remove the parenthetical figure references from your subheadings. For example, headings like "3.4.1 PCC (Fig 5a)" and "3.4.2 TCDF (Fig 5b)" are not standard for academic journals. Change these to simply "3.4.1 PCC", "3.4.2 TCDF", or use a descriptive phrase. You can refer to the figures within the main text of those sections instead.
4. Underlined Sub-headings (Sections 3.4.1 to 3.4.4) You have used underlined text to act as inline sub-headers (e.g., Causal drivers and Non-causal drivers). This formatting is not standard for final publication. Please remove the underlines and either format them as standard sub-subheadings or integrate them into the paragraphs as complete, coherent introductory sentences.
5. Table Caption Placement Currently, the caption for Table 1 (and potentially others such as Table 2) is placed at the bottom of the table. Standard journal formatting requires all table captions to be placed above the table. Please check and adjust all tables in the manuscript accordingly.
6. Minor Typographical Errors
• Line 48: Please delete the unnecessary comma in "Second, is..." so it correctly reads "Second is the old problem of...".
• Line 73: Please add the word "for" after "account" so it reads "do not account for auto-correlation".
• Line 176: There is an unnecessary comma immediately preceding "Fig. R1" (or the figure reference in this section). Please remove it.
• Line 236: The abbreviation "etc," should be correctted to "etc., ".
• Line 903 (Section 5.3): The phrase "in different time period's" contains an errant apostrophe. Please correct this to "in different time periods".
I look forward to receiving your revised version.
Yonggen

The authors cleared all the comments, and the manuscript is ready for publication.