I am excited to see this type of model developed for investigating circulation, sea ice, and productivity in the Canadian Arctic Archipelago (Jones Sound in this case). I would like to share my own experience with modeling flows through the CAA. Previously, I used a coarse-resolution model to investigate these flows, but I have since recognized the critical need for a high-resolution model to accurately capture detailed current patterns and better understand the circulation and water properties in this region. The authors have done an excellent job in developing this high-resolution model. It is generally understood that the variations of transports through CAA are mostly controlled by changes in the large-scale circulations, and it would be beneficial to mention this.

While acknowledging the impressive work, I believe there is still potential for further model improvement. For instance, addressing the warm bias and resolving the model crash issue within the biogeochemical component would enhance its accuracy and reliability. The authors did not investigate the cause of this biogeochemical model crash. While not strictly necessary, providing some insights into this issue would be valuable for the scientific community.

Specific comments:

• Line 65: “?” is needed at the end of the (2)
• Lines 32-33: 2m air temperature is used in driving the model, but why 10 m air temperature is used here?

The study by Pelle et al. investigates ocean conditions, sea ice and biogeochemistry in Jones Sound located in the Canadian Arctic Archipelago. Although Jones Sound is one of the three connections between Baffin Bay and the Arctic Ocean, it did not receive so much attention. This is mostly because of the small scales of the inflow and outflow gates, which are very difficult to model, and its remote location. Here, the authors developed a very high-resolution model setup based on MITgcm that well resolves the complex structure of the ocean conditions in this region. The study is interesting and novel, and contributes significantly to our (limited) knowledge of this region. The manuscript is well written, relevant literature is cited, and the figures are generally nice. However, I am not sure that the calculation of volume transports is correct. This should be clarified. For this reason, I would recommend major revisions.

General comments:

* The model simulation stops in 2016. Would it be possible to extend the simulation until recent years?

* It is a bit confusing that you use two MITgcm setups here, plus the NEMO simulation used for the boundary conditions. Why is the low resolution MITgcm simulation needed? Can't you apply to boundary conditions from NEMO directly to the high resolution MITgcm setup?

* My major point concerns the volume transports described on page 11. I am quite confused about that. The net flow through Jones Sound should amount to zero, otherwise there would be an accumulation/volume loss. So why is the net volume transport (Figure 6a/b) not zero? Is there a major contribution from runoff? I also find the sentence in line 192-194 confusing, as the sum of the absolute value of inflow and outflow is not very meaningful. Please clarify. The sentence in the abstract (lines 7-9) should also be checked. Is this related to the way you apply boundary conditions (no flow at boundaries) in the model?

* The discussion section reads in parts like a conclusion. It could be made clearer what is actually discussed here. Maybe adding subtitles would help.

Detailed comments:

* Line 12: the 11% reduction, is this for the time period 2003-2016? Maybe add the time period here.

* Line 28: add a reference for the 0.3 Sv for Jones Sound

* Lines 64-66: The points are a bit out of context, since you already stated the aims of the study in Lines 57-60.

* Line 168: remove "and 2019"

* Line 217: why do you take 150 m? Instead of taking the upper 150 m, you could take T=0°C as a threshold and plot the mean circulation in the water layer with T<0°C.

* Lines 273 and 275: should this be ice area and not extent? In the figure ice area is shown. It would also make sense to define "ice area" somewhere in the text. 

Line 294: abbreviation should be NCP

Line 337: --> importance of circulation in Fram Sound

* Line 346: --> ...declines on average

* Figure 3: The plots showing observed and modeled profiles is not very clear, there are too many lines on top of each other. Maybe there is a better way to visualize the comparison.

* Figures 4 and 5 could be plotted in the same style, that would look nicer.

* Figure 7: the arrows are very hard to see. Is it possible to increase the panel size (descrease the space between panels)?

* Figure 9 caption: c-d is volume, and not extent, right?