I think this is a useful and well-described model. I cheer the authors for putting so much effort into the description of the model, although I did not feel like I could meaningfully review the aggregation module. My main concern is that despite the substantial effort to describe the model, the testing of the model is somewhat limited. I think the hypoxia/oxygen comparison is helpful, but I would like to see more justification for the benthic module and more detail presented on the Black Sea ARGO comparison. General and detailed comments are listed below.

General Comments:

Is the benthic module really much better than a reflective model? There is not accumulation of solutes, sorption, etc, so maybe there should be a discussion as to how this module would compare to a simple reflective model, like the one in the Fennel ROMS biogeochemical module? As I read lines 620-625, there seem to be even more assumptions and ‘fixes’ made to permit the incorporation of the benthic module. Part of this discussion or consideration should be whether this benthic module could store materials seasonally or long-term, as otherwise it may not offer much real mechanistic value. I can see in the application that the model produces seasonal changes in sediment-water exchanges, presumably due to the temperature effect on remineralization, but there are not enough observations to indicate if this is correct. The model may get a relative magnitude of the sediment solute fluxes, but the time variation is super important to justify the somewhat complicated approach to the benthic module.

I found the application of the model in the Black Sea to be superficial and unsatisfying. Can the authors offer a little more sensitivity analysis of processes related to these variables and how this changes the comparison? This paper is meant to highlight this model, and despite an enormous amount of text describing the model, there is very little analysis to show how well it works.

Specific edits/comments

Line 45: “sesaonal” is incorrectly spelled

Line 61: I think the authors should also not that parameter definitions are provided in Table 2

Table 1: “Silicilic” should be “Silicic”

Benthic Module in table 2: for Panox, the word “Fraction” is missing an F

Line 117: I think there needs to be a section describing the chlorophyll module in more detail? In Table 1, the reader is given the impression that chla is simply a fraction of each process, and it is unclear how this differs from assuming a C:CHL ratio. But now I see there is an entire section on the Chla content and that should be cited here.

Line 132: Is there any further information to give on how the IOP model was tested? In a supplemental material, perhaps.

Line 191: The sentence “In case of carbon limitation, when bacteria do not require to consume NHs for DOC consumption,…” I think should be “In the case of carbon limitation, when bacteria are not required to consume NHs for DOC consumption,…”

Figure 3: Why is the are the gelatinous pools not connected to the other variables in this diagram?

Line 200: by “variable” do you mean that the C:N ratio varies in time, or that the ratio varies by organic matter type? Please clarify

Line 232: I think it is confusing to describe the ODU as partitioned between the reduced substances. You don’t actually model them and their portion is not represented in the ODU production term in the model. I suggest removing this detail. Further, I think Table 3 is not helpful, because not all of these equations are actually modeled. It therefore confuses the reader who might not realize these processes are not being modeled. Simply describing the simplification to ODU is sufficient.

Line 236: I recommend that the detailed kinetic equations are broken up so that they are in the manuscript where they are described. On this line, I need to scroll down several pages to get to Eqs 83-86.

Line 386: Are there no temperature dependencies of gelatinous zooplankton? I suppose this is system specific, but these organisms are highly seasonal in temperate systems.

Line 528: “produces” should be “produced”

Paragraph beginning on line 537: So were these parameters estimated once by this approach and now fixed values are used in the module? If so, please say that. It gives the impression that the monte carlo simulation might be a dynamic part of the model. After seeing the equations, I guess they are just linear regressions that were previously developed? I guess I am just recommending that you describe this more clearly.

Line 698: There is an unnecessary space after “Then”

Line 713: “Precipitation” should not have an “s” at the end

This study describes a biogeocehmical model for simulating dissolved oxygen and benthos including detailed formulations and parameters. This model is especially well presented including sufficient details. I appreciate the author's efforts making the model clear, well explained, and open-source for the readers. I have a few comments and suggestions before the manuscript is ready for publication

1) Section 2.1, please indicate the reason of having three phytoplankton groups. What is the biomass/proportion of these three groups? What are the different roles of these three group in oxygen cycling and benthic activities? In Figure 1, please change nanophy and microphy to nanoflagellates and microflagellates. Otherwise it is confusing because also diatoms have both size catogoties, nano and micro.

2) Why do the shelf data in 5.1 last only till 2002? Any recent bottom DO observations in WOD?

3) Section 5.2, can you show how much the halocline is overestiamted? Any suggestions on how to improve the overestimation of the halocline?

4) Please add some discussion on how well the presented DO and benthic model is compared to other models with similar fuctions, e.g., in complexity and model performace.

5) L 737, any likely explanation why the model overesitamtes DO in most years?

6) Would be great to include validation of bottom temperature and surface DO to help interpret the model performance presented in Fig. 6-10.