This article is discussing the development and validation of an ocean-bio-geochemistry model customized for the north Indian Ocean. The authors make a good effort to get the simulations done and for the validation, and is publishable. Modelling ocean bio-geochemistry is very difficult and many models still struggle to get the bio-geochemistry right in those simulations. However, I have some concerns, which need to be addressed before it can be accepted.

Major:

1. I do not see any wind simulation and its validation in the model. Since the monsoonal currents dictate the dynamics and associated processes in NIO, the wind simulations and their assessment are very important and must be presented in the main text.

1. I thought, generally the models have relatively good simulations for surface Chl-a and compare well with the satellite and Argo data, which is not the case here in your model simulations. It is good to have a discussion based on other model simulations for NIO and other oceanic regions for Chl-a comparisons. Please see this and mention such model simulations and validation: https://doi.org/10.1016/j.ocemod.2024.102419
2. There is a subsurface maximum for Chl-a in the NIO. Please show the model simulations and comparison with Argo measurements.
3. L459: If the model overestimates, how that would affect the OMZ in AS and BoB? Which oceanic region has large OMZs? L463, you say that in AS, it is well represented, but BoB overestimated. Fig 16 provides no clue that any basin is better for this. Also, why the equatorial region has such a big difference?
4. Write the validation information with bias values in the abstract
5. Developed or customized the model, please make sure that you use a correct word for this
6. L336: reproduced is a “lighter” word; how good is the comparison? Please write some numbers.
7. LK353: Why the Chl-a simulation is not good in the Somali coast or western Indian Ocean? Summer Chl-a is even worse?
8. L371-372: How did you arrive into this conclusion; is this about the size of the plankton?

Minor:

L4:  north of 8S? It can be anywhere north of that latitude. Please be specific

L22: and is missing

L23; separate the Roy citation from the bracket

L40: about the NIO stressors: https://doi.org/10.1016/j.pocean.2023.103164

L53: models are “tools” for studying

L55: this is another model validation for this region: https://doi.org/10.1016/j.ocemod.2024.102419

L85: coordinates of the region

L113: salinity from 1998 data, any updated version?

L115: How long was the spin up and when did the model stabilize? Which year onward you analyse the model results for science?

L119: citation format is not correct

Figure 1: rivers can be in red color, to differentiate from the bathymetry blue color

L147: any reference for this? Overestimation and scaling have got any criterion? Why 25%?

L175: not from WOA 2023?

L176: CO2 is increasing, so the old climatology values are good?

L192: SSP 5-8.5 is an extreme case. So how much that would influence your simulations?

L223: How the adjustments are made? Just random or any criterion followed?

L243: citation format is not correct

L274: SST has been already defined

L276: particularly and especially, Please rephrase

Figure 4: Why summer MLD is bad in the model?

L337: SSS has been defined already

L350: Narmada-Tapti

Fig 17: How that affects simulations of SLA?

L495-500: remarkably well? Not sure, if you look at the SLA figure.

L514: IOD has been defined, as for L528: RAMA, OISST

579-580: model is good because of its good bio-geochemistry simulations? What about the model physics?

L584: a detailed account of winter blooms are here: https://doi.org/10.1016/j.jenvman.2023.117435

L588: different response? please be specific

This manuscript presents a coupled ocean dynamics-biogeochemistry model whose domain covers the Indian Ocean north of 8°S with a grid resolution of 1/12°. The model’s performance is evaluated through comparisons between model results for the years 1980–2020 and observations.

While it is clear that a considerable amount of work has gone into the development and validation of the model, I feel the manuscript reads more like a report than a journal article and is thus not yet ready for publication. I believe the discussion needs to be more developed on: 1) what is new about this work and 2) what are the possible causes for the model not performing as well in some aspects as in others. The authors do discuss the ways in which the current version of their model performs better than an earlier version, but I am curious about how this model is different, in terms of setup and/or performance, to other physical-biogeochemical regional models of the northern Indian Ocean, such as that of Sunanda et al. (2024). In addition, how do regional models of the Indian Ocean perform in comparison to global models? The authors state in Section 1 that the state of the Indian Ocean tends to not be reproduced well in global models, but how do performances of past regional models and MOM6-COBALT-IND12 v1.0 compare to that of global models? What are the possible causes for discrepancies between observations and simulations for fields other than chlorophyll?

The following are more detailed comments. I do not have time to list all the grammar and punctuation errors because they are too numerous.

Line 21: I suggest adding your definition of “northern Indian Ocean” here, because the inclusion of Tanzania among nations along its coast is confusing for readers who assume the term refers to the portion of the Indian Ocean north of the Equator.

Line 23 and elsewhere: When a set of parentheses include both explanatory text and citations, I believe the correct format is to end the text with a semicolon.

Line 89: There seems to be a mistake in the citation.

Line 91: How does this manipulated depth differ from the real depth? Is the cross-sectional area of the channel conserved?

Line 112: How well does the model reproduce the observed sea surface salinity without the restoring? Are there spatial variations in the differences between the restored and unrestored salinity values?

Line 120: I suggest reserving the term “boundary condition” for the scheme by which the boundary condition is specified, which is different from the values that are specified.

Figure 1 caption and elsewhere: There are no sections in this manuscript called “Methods” so references to this non-existent section should be changed.

Line 126: ORAS5 is not yet defined at this point.

Line 176: “Initial DIC and alkalinity were initialized” does not make sense.

Line 177: Having “a small impact” is different from having “a negligible impact” or “little impact”. Which do you mean?

Line 198: What is meant by “long-term decadal”? Long-term as well as decadal?

Figure 3 and elsewhere: I suggest not using the word “data” to mean observations.

Line 246: What is the source of the updated data?

Line 287: How is the surface heat flux calculated in this model? What are the inputs?

Lines 292 and 293: Are these directions stated correctly?

Lines 308 and 422: I suggest labeling these places in Figure 1.

Section 4.3: Why are arrows IX through XII included in Figure 7 if they are not discussed?

Lines 360–362: I suggest rewriting this sentence to clarify the proposed relationship between 1) low surface chlorophyll and 2) the weak seasonality of surface chlorophyll on one hand and 1) strong stratification, 2) lower nutrient supply, and 3) the presence of the subsurface chlorophyll maxima. Do all three proposed causes affect both aspects of the surface chlorophyll?

Line 397: What is meant by “northeastern Arabian”?

Line 403: What is the definition of a shadow zone?

Lines 462–465: What is the definition of hypoxia used here?

Lines 523 and 547: “opposed” is not the correct word to use here.

Lines 559–560: The positive primary production anomaly in the Arabian Sea is much smaller in the model than in observations. What might be the causes for this?

Appendix: The title as well as some of the figures are in the wrong places.