This study investigates the roles of topography and vegetation in hydrological processes within cold alpine basins of the Mongolian Plateau using a stepwise FLEX modeling framework. This manuscript presents a valuable contribution to cold-region hydrology in Mongolian Plateau. The research is scientifically sound, methodologically rigorous, and addresses the gap in hydrological modeling for data-scarce, cryospheric regions in Mongolia. With the suggested revisions—particularly in methodology clarity, discussion depth, and figure improvements—it will be suitable for publication. The manuscript falls between minor and moderate revisions, with the following specific recommendations.

Comments

1. The background is well-presented, but the uniqueness of the study area (e.g., extreme climate, sparse vegetation, and cryospheric dynamics) could be emphasized more to justify the novelty. Moreover, this work aligns well with the objectives of the new IAHS HELPING (Hydrology Engaging Local People IN one Global world) Decade (2023–2032), which emphasizes interdisciplinary approaches to address local hydrological challenges. I recommend to add this in either the Introduction or the Discussion.
2. The literature review should include more recent studies (post-2020) on cold-region hydrology, particularly those addressing snowmelt and vegetation interactions in similar environments (e.g., Central Asia, Tibetan Plateau).
3. The similar performance of FLEX-T and FLEX-D is attributed to low vegetation heterogeneity. However, is this finding generalizable to other basins with higher vegetation variability? A comparative discussion would be valuable.
4. Line 428-433: Please provide the exact dates (year, month, and day) of these two precipitation events to enable a more precise understanding and validation of the related hydrological processes.
5. The discussion should explicitly address limitations, such as the lack of direct validation (e.g., snowpit measurements, isotope tracers) and the impact of data scarcity on model uncertainty.
6. Line 582: Provide a clearer explanation of the relationship between the proportion of snowfall in precipitation (Ps/P) and the contribution of snowmelt to streamflow (QM/Q), while ensuring that the related terminology and trend descriptions are accurate and consistent, to enhance the coherence between figures and text, as well as overall readability.
7. Line 673-675: The description of high infiltration rates in dry grassland soils leading to reduced runoff in arid regions is rather general; it is recommended to provide relevant references to strengthen the argument.

Minor Comments

1. Some acronyms (e.g., SWE, HRUs, NDVI) should be defined at first use.
2. The use of technical terms throughout the manuscript should be consistent (e.g., “modelling” and “modeling”, “elevation zones” and “elevation areas” ).
3. Line 193: The URL http://srtm.csi.cgiar.org is hosted by the CGIAR Consortium for Spatial Information (CGIAR-CSI), rather than the International Center for Tropical Agriculture (CIAT). Please revise the data source attribution to reflect this accurately.
4. 3 illustrates the elevation band division based on DEM data, it would be more appropriate to place it in Section 3.2.
5. Some figures (e.g., Fig. 5, Fig. 8) need clearer labels and legends. Fig. 13 needs better visualization.
6. Line 692: "soi/rock" should be "soil/rock".
7. Please correct the punctuation errors (e.g., Line 637, Line 711 ).
8. The conclusions are well-supported but should be more concise.

This manuscript investigated the impact of topography and vegetation on catchment hydrology in two cold mountainous basins of the Mongolian Plateau using stepwise top-down modelling approaches. It is very interesting and scientifically sound. Also, it is suitable for Hydrology and Earth System Sciences. However, some improvements are still required.

Detailed comments

1. The annual precipitation is ~200mm and ~160mm in the two basins, which belongs to sub-arid region. Therefore, most quick runoff should generate from infiltration excess runoff. On the other hand, in the FLEX, runoff generation is described as saturation excess generation. The reliability of the conclusion and the rationality of the method should be further assessed. At least, more explanations and discussions are requested.
2. This study selected two alpine Basins as the study basin. In the study basins, there is only one meteorological station for each basin. To represent the spatial variation of precipitation, the authors a precipitation increase rate of 4.2% from the Heihe River basin in China. Does the precipitation increase rate of 4.2% conform to the study basins? More explanations and discussions are requested.
3. In the study basins, winter temperature falls below -30 degree. It’s better to discuss the impact of frozen soil.
4. Lines 259-260, there is a mistake on the description of the method for actual evaporation, i.e. “Ep” should be “Ep - Ei” (potential evaporation minus interception evaporation).
5. The authors conducted relevant researches in other alpines basins, such as Heihe River basin. In this study, it's more useful to discuss both the similarities and the differences in order to gain a clearer understanding.