The authors downscaled two future climate projections to the Atlantic Canada domain to characterize the future states of the physical and biogeochemical environments. Their results show quite different outcomes of future climate states in the region. While the topic is interesting, the manuscript is mostly descriptive and speculative and does not provide much insightful new knowledge or sufficient explanations of the results. Because it is known that future climate projections can be widely different across models (hence we have CMIP), downscaled projections to a regional model being different should not be surprising. The weakness of this manuscript, however, is the lack of robust connections showing that the changes of circulation (shelf-break currents) cause the different biogeochemical projections. For example, how does the changes in the shelf-break currents affects the temperature and salinity over the shelf? Note shelf-break currents and along-shelf currents are different. Tracer released over the Labrador continental slope is expected to move along the slope and shelf-break, however, tracer concentrations from the two simulations doesn’t explain the changes of physical and biogeochemical environment on the continental shelf, which seems to be the focus of this manuscript. A more relevant analysis can be to compare the distribution of ENS tracer (on the shelf). To understand the causes of the simulated temperature and salinity changes, budget calculations including the along-shelf and cross-shelf advective fluxes as well as air-sea fluxes are needed. Otherwise, claiming shelf-break currents causing the changes is unsupported. Similarly, how the diverging projections of temperature and salinity lead to diverging biogeochemical projections, e.g., PH and DIC, needs to be supported with actual analysis.

Other comments:

Line 18: “Our results illustrate that a wide range of outcomes is possible for continental margins” This is extrapolation and unsupported.

Line 61: “Future projections indicate a significant decline in SC strength over the next century potentially accelerating warming and deoxygenation (Saba et al. 2015, Claret et al. 2018).” Isn’t the projection of SC strength model-dependent, as mentioned in the abstract?

Line 231: “This localized increased inflow creates an even larger disparity between the southwestern and northeastern Scotian Shelf than what is currently present”. Localized increase inflow is not shown. This statement (and the paragraph) is unsupported.

The study uses a regional ocean model to investigate how the future ocean conditions in the northwest North Atlantic, like the emergence of warming and acidification, are controlled by climate-induce changes in the local circulation. The study demonstrates that a plausible increase in the slope water contribution to the Scotian Shelf associated with a weakening in the shelf break current, can drive enhance bottom water warming and salinification, and lead to localised regions of reduced/increased acidification (with less acidic regions being co-located with warmer regions).

The study will further our understanding of the response of the shelf seas and coastal regions to climate change (which currently is poorly understood). The use of somewhat “idealised” and targeted simulations (e.g., forcing the regional model projections with the same biogeochemical conditions but different physics-dynamics-circulation conditions), in my opinion, is a strength of the study and enables to inform on control mechanisms. The conclusions are well supported by the analysis and figures, and to the most part the manuscript is well written. However, the description for the implementation of the downscaling experiment is difficult to follow (at least to me) and I am still unsure if I understood the implementation of the forcing for the projections with the regional model correctly. Hence, I recommend the following revisions for clarity.

Specific Comments

1. Description of the downscaling experiments with the regional model: I suggest that section 2.2 is reorganised, restructured and re-written for clarity. I suggest that section 2.2 is separated into two subsections that each separately describe the two experiments: 2.2.1 downscaling using forcing from the GFDL-1%pCO2 increase per year for both physics and biogeochemistry; and 2.2.2 downscaling using forcing from the DFO under RCP 8.5 (to me the DFO model projections and their set-up was somewhat unclear) for the physics but using the GFDL-1%pCO2 increase per year for the biogeochemistry. Please see specific comments below, but consider re-writing the entire section as to provide a clearer description for the set-up of your experiments.

1.1 Lines 101-103 and 117-119:  To me, it is not clear what “adding the anomaly (or delta) to the 1999 distribution or to the 1999 initial file” means and what this 1999 initial file/distribution corresponds to? Do you mean that the trend from the GFLD projection (essentially the de-seasonalised anomaly at 2065 relatively to 1999) was added to the 1999 conditions from the present day run with the regional model? Or do you mean that this trend was added to the 1999 conditions from the GFDL run itself (such as to keep a constant seasonal cycle?). Please I suggest that you clarify what this 1999 initial file/distribution corresponds to.

1.2 Lines 120-121, surface and lateral boundary conditions: I am confused here. If I understood correctly, for the boundary conditions you do not use the same approach of adding “deltas” as for the initial conditions? If yes why not? Also, the text implies that for the ocean boundary conditions and atmospheric forcing you use directly the de-seasonalised GFDL outputs such that the imposed atmospheric and oceanic forcing for the ACM projections does not include any seasonal cycle? I am not sure that makes sense to me, so probably I have misunderstood of how the atmospheric and oceanic forcing is imposed at the open boundaries in the future time-slices experiments. Please, I suggest that you clarify/re-write how the atmospheric and oceanic forcing along the open boundaries is estimated and imposed in the regional model future projections. Also, it will be useful to clarify which atmospheric fields are used to force your simulations.

1.3 Lines 124-125, DFO future projections: I am unsure what you mean by “six IPCC future climate runs”, (maybe from 6 CMIP5 Earth system models?). Please, I suggest that you clarify.  

1.4 Lines 131-132: This text suggests that only the air temperature and precipitation from the DFO RCP 8.5 projection are used as surface forcing for your downscaling experiments? What about winds, humidity, radiation? How are the other atmospheric fields/forcing imposed in the regional model?  

1.5 Lines 133-135: To me it is not clear why and how the conditions/fields along the lateral boundaries were averaged to get the delta added to the 1999 initial field. Are the anomalies/deltas (that are added to the 1999 initial fields) in the interior of your regional model extrapolated from the conditions along the oceanic lateral boundaries? To me that does not make so much sense and it will not lead to appropriate or consistent-to-the-forcing initial conditions for the time-sclices projections. I presume that I just have misunderstood as it is not clear and can you please re-write this part for clarity.

2. Line 163 and Figure 2: Why were 9 months chosen as the timescale for which to present/discuss the averaged concentration of Labrador Sea dye after dye tracer initialization? Is this 9-months timescale relevant in terms of the Labrador current velocities and shelf-lengthscale (i.e. travel distance) arguments? If you could please clarify.

3. Figure 2 and lines 165: In my understanding Figure 2c shows only the decrease in LS concentration in the future projections, rather than the change in the future minus the present day (such that regions of increase are not shown). Comparing Figure 2a and Figure 2b it seems that they should be regions of increase in LS concentration, especially in the AMC-DFO. This can be confusing and makes it difficult to judge if the amount of LS dye moving along the shelf break declines for the AMC-DFO. I suggest to update the figure to show the actual change (increase and decrease) rather than just the decrease.

4. Lines 227-228: I am not sure how accurate is this statement. In my understanding, the two simulations have also very different atmospheric conditions/forcing in the future. Are the heat, momentum and freshwater air-sea fluxes similar in the two ACM-projections? If not, I suggest to clarify that the similarity of the air-sea CO2 flux in the two ACM-projections implies that “the shelf-break current strength is less of a control for the surface carbon budget” (rather that generalise to “water properties”).

5. Figure 5 (typo in the caption): I believe you mean “Figure 5: Left panel … ph. Right panel….

6. Table S3 in the supplementary Information: For clarity, I suggest you mention in the caption that positive values indicate flux from the ocean to the atmosphere (i.e. outgassing).

7. Figure S3 in the supplementary information: In the caption it is mentioned that “Open symbols indicate predicted values and filled symbols indicate actual simulated values”. Can you please clarify what you mean by predicted vs simulated values here? Also, to me it seems that only filled symbols are shown in Figure S3. Additionally, I am unsure about the meaning/interpretation of the lines connecting the symbols, and of the arrows with the SLE text in Figure S3a and b. If you could please clarify what these lines and arrows represent/highlight (maybe in the caption) that would be very helpful.

General comments:

The authors compared two downscaled climate model projections to evaluate the mid-century physical and biogeochemical responses in the northwest North Atlantic shelf region. They demonstrated that the two models resulted in largely different changes in along-shelf circulation that contributed to varying patterns of warming, salinification, and increased/decreased acidification.

The manuscript is well written and, to my knowledge, cites the necessary bibliography. The methods are well described and the regional model used in the manuscript is well-validated and is adequate to answer the proposed questions.

In the manuscript, the authors show that changes in along-shelf transport in the two future scenarios are not similar. While ACM-GFLD shows a nearly 70% decrease in southwestward along-shelf transport in the Scotian shelf associated with the disappearance of Labrador Sea dye in the region, ACM-DFO shows nearly no change in transport and only a 33% decrease in LS dye. The literature demonstrates that the replacement of LS water with Slope Water does impact bottom temperature, salinity, and dissolved oxygen concentration in the shelf, particularly in the channels and deep basins of the Gulf of Maine and Gulf of St. Lawrence, which partially backs the results in the study.

While this is a robust result that advances knowledge, I think that linking short timescale changes in shelf properties solely to these changes misses one step. For example, it is not clear to me how the different changes in ocean circulation shown in the two projections are responsible for the patterns in bottom pH. Furthermore, why are the results for the surface properties missing in the analysis? It seems like surface temperature is only briefly mentioned in lines 227-228. I believe that the missing piece that establishes the causal relationship between changes in ocean circulation and diverging biogeochemical projections could be mitigated in one of two ways: (1) the more robust calculation of fluxes and budgets on each shelf region (GoM, SSsouth, SSnorth and GB) or (2) a more anecdotal demonstration of this relationship, perhaps following the inflow of LS water and Slope water and the consequent changes in pH and DIC.

Specific comments:

Lines 46-50: The description of the objective of the study at this point seems redundant with the last paragraph of the Introduction. I'd suggest incorporating these sentences in the last paragraph or removing them.

Lines 149-151: Again, I do not think that it is necessary to repeat the objective of the study, especially in the Methods section.

Lines 227-228: The authors should add that surface temperature changes are not shown and air-sea CO2 flux changes are shown in Table S3.

Lines 263-265: Maybe it's my lack of knowledge of ecology, but it was not clear to me why Atlantic cod and snow crab would see larger habitat shifts in the southern subpopulation in a scenario with an unaltered shelf-break current.

It seems to me like Figure 3 and Table S1 give the exact same information, so one of them can be removed (the references in the text have to be adapted accordingly).

Figure 5: I am curious as to why the authors chose to use blue for positive and red for negative differences (especially on panel e).

Figure 5: Why didn't the authors show the difference between ACM-DFO and ACM present, as they did for ACM-GFDL in panels C and D?

Figure 6: Why didn't the authors add the present-day pH values to panel B?

Technical corrections:

Line 174: Reference to Figure 4 should be Figure 3.

Line 221: Reference to Figure 4 instead of Figure 5.