This manuscript is a combination of a drilling report from two boreholes in the Bedretto Tunnel, combined with laboratory measurements of physical properties on core samples from those boreholes.  This is a nice description of the field measurements, including in-situ hydraulic testing, and a comparison with lab permeability measurements.  I agree with the importance of establishing the geologic and geophysical context of the boreholes before more ambitious testing takes place.  This is a solid report and I found nothing highly problematic, with the caveat that I am not really an expert on in-situ hydraulic testing. 

Main comments:

Composition of the material was discussed, and from the descriptions of the different facies that the mineral composition changes with proximity to the fault core.  Since permeability is strongly controlled by mineralogy, I think the composition of the samples needs to be reported.  I see in the appendix that there are XRD measurements, so please present the modal abundances of each mineral (abundances of < 5% don’t need to be reported).

The text on L376-379 reports that the effect of increasing effective stress during the lab permeability tests is larger for the more impermeable samples compared to the more permeable ones.  This is a counterintuitive interpretation that I don’t think is correct, and is probably and effect of different scales in Fig. 8.  The decrease in permeability with increasing effective stress in Fig. 8a and 8b look large on the log scale, but they will be negligible compared to the samples in 8d that have an absolute permeability value on the order of 10^-12 or even 10^-16 m².  Conversely, what looks like a negligibly small difference in 8d could still be orders of magnitude larger than any change in the other three panels. Because the absolute values of permeability are very small in low permeability samples, the figure actually shows that the effect of increasing stress is correspondingly small.  I would refrain from comparing the stress sensitivity of the samples and only comment on the stress sensitivity for an individual facies or group of samples where the absolute values of permeability are on the same order.

I couldn’t quite follow the discussion on L404-424.  The trend in Fig. 10 can be clearly attributed to sampling bias, so I am not sure what the argument is here.  Is the argument that there is still a scale-dependence of permeability even without sampling bias?  I can imagine that small-scale measurements of permeability will have a very wide range if the sampling bias were removed such that large fractures were also being sampled, but if the sampling density was large enough to approximate the fracture network distribution at large scales, the large-scale permeability could be accurately determined.  Of course, this is difficult and not practical at the moment.

L35: “types” rather than “appearances”

L87-90: I’d like some more detail on how these RG1 and RG2 designations came about.  Are they simply end members of the granite composition?  Or are they from specific sampling sites or sampling strategies? Also, I would consider the proportion of the mineral types to be part of the composition, so it is confusing/misleading to say that the composition does not vary.

L101-106: I think it makes sense to switch Fig. 2 and 3, and indicate where the borehole images came from.

L127-128: What do you mean by cohesive or non-cohesive fractures?  Cohesiveness is a mechanical behavior and not really something that can be described visually.  Or do you mean open or filled fractures, or something similar?

L173: What is the composition of the core samples?  RG1 or RG2?  Is there some basic XRD measurement available that quantifies the main mineral phases?

L181-183: I suppose this means that the core samples here are isotropic and do not need to be oriented?  Or were they recovered at a specific orientation?  I suggest adding a sample photo to Fig. 4.

L190: low permeability

L311: due to…?

L313: Please define P₁₀ and how it was determined.

L320,354: Please provide a facies legend for Fig.6 and 7

L451-452: This mention of pore pressures comes a bit out of nowhere, it would be helpful to re-state the values here and add some discussion to give the values context.  What are the expected hydrostatic pore pressures?  How large are the overpressures (i.e., what are the lambda values)?

Major comment:

The article presents a study on the multi-scale hydraulic and petrophysical characterization of a heterogeneous fault zone with in the Bedretto Laboratory, serving as a foundation for site selection and preparation for the FEAR experimental injection. The study was motivated by the necessity to accurately constrain fluid migration paths in crystalline basement rocks to effectively plan controlled stimulation experiments. Its aim is to quantify variations in hydraulic properties and structural heterogeneity across scales by combining field-scale with laboratory-scale analysis performed on retrieved core samples. From the observations, the authors characterize the fault architecture, identifying the fault core, and demonstrate a pronounced scale effect. Overall, the manuscript is written clearly, and the conclusions are well-supported by solid data, providing practical guidelines for the upcoming FEAR experiments.

Minor comment:

Line 35-59: The opening paragraph starts with a very broad overview of earthquake hazards and societal impacts, then illustrate the difficulty in predicting earthquakes and the reasons behind. However, the transition from earthquake to hydraulic testing feels somewhat abrupt, there is a missing logical link explaining why hydraulic characterization is a critical step for the stimulation experiments. Also, the current content lists permeability (line 45) as one of many factors in the complex system, it would be beneficial to emphasize it to have a smoother transition of the topics.

Line 309-311: “Moving away from the … due.’ This is an unfinished sentence, please recheck it.

Figures 6 and 7: These figures would be much more readable if the facies legend were included directly, avoiding the need to scroll back to previous sections.

Line 376-379: The text states that effective stress impacts tighter facies more intensely than high-permeability ones. However, this conclusion is difficult to verify visually because the plots in Figure 8 span vastly different permeability ranges. A slight visual reduction in the high-permeability samples (Fig. 8d) might actually correspond to a much larger absolute reduction compared to the tighter facies. I suggest clarifying this conclusion to avoid potential misinterpretation.