The paper describes a novel application of large-scale MOM6 to Great Lakes region (Lakes Michigan and Huron in particular), and assess its performance against observed temperature profile, currents and seiche signature. The paper is well written, logical, and provide a good historic prospective on the challenges and successes of GL modeling. I only have some relatively minor comments.

• They mentioned that the new VCSs “largely eliminated the need for bathymetric smoothing” and cited Morey et al. (2020). I read thru that paper and the related papers on VCSs, and actually they all mentioned the challenges they faced in representing the steep bathymetry, and that smoothing was a major error source. So this reference and sentence should be revised;
• The baroclinic time step was shown, but how about the external time step (I think MOM6 uses splitting)?
• The albedo shown in Table 1, 0.33 seems too large?
• I understand they did not add river flows and evap/precip. Can they comment on the challenges in doing that, specifically, the largest rivers connecting Superior and Lake St Clair? Would the omission be a factor of underestimation of through flow in Strait in MOM6?
• Table 4, 6 have mis-aligned columns: no MBE for z*, 2 MBEs for FVCOM;
• They compared the dates for summer stratification and fall overturn, but need to clearly show how they calculate those times;
• Line 357 mentioned “observations exhibit flat-lined behaviour that is indicative of instrument noise floors”. Could this be short-period internal waves?
• Near Line 405: should add reference to Fig. 12. Line 564: ‘12m’ is confusing; change to 12 million.

The manuscript presents an interesting and relevant study on the development of model configurations in the MOM6 general ocean circulation model for the Great Lakes. The work highlights the sensitivity of different vertical coordinate systems (VCS) available in MOM6 and compares the simulations with satellite observations and outputs from the well-established LMH-FVCOM model. The study is generally well organized and scientifically motivated. However, several important issues require clarification and further analysis before a final decision can be made. The following points should be addressed to improve the rigor, clarity, and overall presentation of the manuscript:

1) Model time step and computational comparison

The time step used in the model configuration appears relatively large. As stated in the manuscript, LMH-FVCOM (with 100 m–2.5 km resolution) uses a time step of less than 10 s. Have the authors conducted any time-step sensitivity experiments to evaluate its impact on model stability and accuracy?

Furthermore, the comparison of processor hours between the two models (lines 554–560) is not meaningful if different time steps are used. A fair comparison would require simulations with similar time-step settings. The authors are encouraged to reconsider this comparison or perform additional experiments.

2) Formatting issue

Please correct the font inconsistency on line 134.

3) Spin-up time

The specified spin-up duration appears short for a lake-scale circulation model. The authors should justify the chosen spin-up time, ideally by presenting LST evolution plots or comparisons with observational products to demonstrate model stabilization.

Additionally, the relatively poor performance in 2017 (after Section 3.4) may be linked to insufficient spin-up. Please clarify whether this was assessed.

4) Closed lateral boundaries and absence of freshwater fluxes

Lines 150–151 indicate that the model uses closed lateral boundaries and excludes evaporation and precipitation. This configuration will affect both radiation balance and water discharge.

Have the authors tested simulations including freshwater forcing? A comparison between the current setup and a freshwater-forced configuration would strengthen the manuscript. Please discuss the implications of excluding freshwater fluxes.

5) Warm bias in nearshore regions (Figure 3)

In Figure 3, the warm bias is particularly pronounced in nearshore regions during summer. Is this related to insufficient vertical grid resolution near the lake boundary or limitations in VCS representation?

Please elaborate on the sensitivity of LST to the vertical coordinate system in these regions.

Additionally, improve the resolution and clarity of Figure 3.

6) Performance of z^* VCS

In Subsection 3.4, the performance of the z* VCS configuration is not sufficiently described. Please provide a clearer quantitative and qualitative assessment.

7) Clarification of statement (lines 380–381)

The statement in lines 380–381 requires further explanation. Please elaborate on the physical reasoning or provide supporting evidence.

8) Water level comparison

In my opinion, the water-level comparison (lines 399–409) is not meaningful due to the absence of freshwater fluxes in the model configuration. Without river inflow, precipitation, and evaporation, water-level validation lacks physical consistency. I recommend removing this comparison and Figure 12.

9) Surface wind forcing (NARR data)

Why was North American Regional Reanalysis (NARR) not tested as a surface wind forcing dataset? Please justify this choice and support the findings with appropriate discussion.

10) Future applications section

Please consider creating a dedicated “Future Applications” section (lines 575–600) to clearly articulate potential extensions and practical applications of the modeling framework.

11) Conclusion – spatial specificity

In Point 1 of the conclusion, please specify that the stated performance primarily applies to offshore regions, as nearshore summer biases are comparatively large.