This study uses a recently completed recalibration of atmospheric hydrogen measurements from 2010 to 2019 to evaluate how well a state-of-the-art chemistry-climate model – that has been used to evaluate hydrogen’s climate effects - represents hydrogen concentrations. Initially, the authors do not consider hydrogen emissions from the hydrogen industry, and then ultimately show that when hydrogen leakage is considered, the model does a much better job capturing the temporal trend. However, the deposition of hydrogen via the soil sink remains highly uncertain, and different model configurations to be more comprehensive are each unable to reproduce trends, spatial gradients, and seasonality.

Overall, I find this paper important, timely, technically thorough and sound, and well-written. As plans to scale up hydrogen advance, it is important that climate modelers are able to perform experiments to assess the resulting climate implications. However, there remain major gaps in our ability to model hydrogen systems. This paper advances our understanding of modeling hydrogen in sophisticated models, which will be increasingly important.

I have one major comment regarding how the manuscript is organized, and several minor comments.

Major comment:

I recommend reorganizing some of the content in the paper; some of the content feels out of place. Specifically, the introduction is really short and I find it does not adequately set up the information needed to understand the methods and results. For example, a key element to understanding hydrogen concentrations is hydrogen sources and sinks. I would expect the state of the science of hydrogen's sources and sinks to be discussed in the introduction, but they are not discussed in detail until the methods, in which they are then mixed in with the references of where the data was taken from. I think it would strengthen the paper if discussion of the sources and sinks was first brought up in the introduction, and then details of model inputs and sourcing would follow later in the methods. Further, I find it a bit odd that the sensitivity methods and results are in the discussion section. I understand that their purpose likely came about from the model results of the base case, and therefore it makes sense chronologically based on the research timeline that they are discussed thereafter. However, as a reader, I want to see all of the methods etc. together in the same section, results in the same section, and discussion in the same section. Right now I had to go back and forth between sections to fully comprehend the experiments and analysis and the takeaways. Therefore, I suggest moving the sensitivity methodology into the methods section, the sensitivity results into the results section, and then leaving the discussion for interpretation and implications of the combined set of results.

Minor comments:

Abstract: “Robust assessment of the climate implications of increased H2 usage in the global economy is partly hindered.” Just a not regarding the use of the word robust – some may misinterpret this to mean that we don’t have robust assessment of hydrogen’s warming effects, whereas the authors’ own recent study (Sand et al. 2023) suggested otherwise.

1-20: “but the increased demand for CH4 may offset much of the expected climate benefit of increased H2 usage” Would be helpful to non-experts if it is briefly explained with the demand for CH4 could offset expected climate benefits (i.e. CH4 emissions)

2-24: “evidence of high concentrations of H2 in many different geologic environments” – my read of the literature is that this sentence overstates the evidence, so I would temper a bit.

2-28: Update to reflect Sand et al. 2023, suggest acknowledging that H2 warming effects are short-lived and adding the value for GWP20 given that challenges of using GWP100 for short-lived warming effects.

2-44: “60+ globally distributed sites.” Are they the locations in Fig 2? Can that be referenced here? Or perhaps a clearer map of the locations is needed beyond just a comparison to model data.

3-56: Reference still in prep?

3-60/63: Again, a map showing this distribution and coverage would be useful.

Figure 1 – I think this figure could be greatly improved. These are prescribed emissions and not model results, or combo of both? The pie slices are not in the order of the legend, nor in the order of the magnitude, making it hard to follow. Why do some values have 1 significant figure and some have 3? Pie charts are also not the best for visualizing data with this many slices, a bar chart would be much clearer in terms of share of each source. Would also make clearer distinguishing the photochemical vs. direct sources (because those can be grouped next to one another), and you could add in the components that are anthropogenic via stacked bars (such as what fraction of methane/biomass burning/etc. are anthropogenic). Also what does “anthropogenic w/o CH4” mean?

4-96: “74.1” – 3 sig figs seems a bit precise, recommend 2.

4-97: “The contribution of other photochemical pathways is estimated by perturbing the associated precursor emissions by 10%.” Not following what is meant/done here?

5-108: This is very valuable info especially as we consider how emissions may change in the future. Would be great if this can be shown in Fig 1.

7-140: “thatH2” formatting

10-166 “In the BASE simulation,80% of H2 emission originate from the transportation and residential sectors (Fig. 6a).” Clarify that this is 80% of *anthro* H2.

This paper addresses an interesting issue related to H2, i.e., processes influencing the removal of H2 from Earth's atmosphere. The aim of the paper is good.

However, I have some major issues noted below:

1. The data used for the analysis here is not published. It includes recalibration of the older data. Until we have that data scrutinized and published, I do not see how this paper analyzing that unpublished data (from a different set of authors) can be published. Bottom line: How can I trust this analysis when I do not know if I trust the observational data used here? As the authors note, some observational data were selected and some were excluded.   Maybe this analysis will hold up when the observational data is published, but I cannot take it for granted.

2. The paper is dense and very hard to follow. The analyses has so many moving parts that I cannot figure out how they homed in on soil uptake as the major issue that is influencing H2 trends.

3. It has no real estimate of uncertainties and discussion of the rather short period of 9 years for the reanalyzed data. The authors just assert some values without justification. 

4. I find the significant figures in this paper hard to swallow, especially when there are no real error estimates.

Some detailed comments:

1. When did H2 from direct mining start and how much does it contribute to the emissions, especially over the period analyzed here? 

2. How well do we know H2 production from CH4 oxidation? Even though CH4 is quite well mixed, what happens after its reaction with OH (that ultimately leads to H2) is very dependent on location and conditions.

3. Is a 9-year trend sufficient to carry out this analysis? Please note that the lifetime of H2, including soil sinks, is reasonably location dependent.

4. It is odd that the people who measured H2 and whose data is being recalibrated are not co-authors of this paper.

5. Given that biogenic hydrocarbons such as isoprene are very short-lived, is the use of monthly climatologies appropriate? First, the yield of H2 from isoprene oxidation is not well known. Even the yield of H2 from formaldehyde photolysis has significant uncertainty. Second, it would depend very much on location and conditions.

6. Let us not forget that the soil uptake is a parameterization!! How good is it? How well is it checked out? (This whole issue is rather circular since the parameterization is not really a bottom-up approach that is tested.)

7. The authors need to pay attention to significant figures. 

8.. I do not understand how good are the trends shown in figure 4. What are the uncertainties?

Knit-picky issues:

How am I to understand a paper which still says "add reference" (line 48)!??