Thank you for the revised version of your manuscript. As you are already aware, since the original referee reports were split on the merits of the manuscript, I asked both of the original referees to look again at the manuscript. I also engaged an additional independent referee for a further opinion on the work.

All three referees have now reported back on the revised manuscript. I am pleased to report that both original referees now agree that the manuscript is publishable. Both also suggest lists of minor amendments that they would like to see before final publication.

Regarding the additional referee’s report, two significant criticisms are raised:

1. The manuscript presents an already described model and contains no new science

2. There are reasons to be sceptical about the broad applicability of a 1D model, particularly in the context of lateral transports of salt and nutrients

On the first point, I am satisfied that the model represents an advance on its predecessor model, and that the manuscript falls within expectations for the science content of GMD publications (this latter point is a perennial issue for GMD). On the second point, I believe that the revised manuscript already tackles the issue of 1D limitations, and it appears to have satisfied referee 2 on this point as well.

Consequently, I believe that the manuscript should be accepted subject to the remaining issues of referees 1 and 2 being fully addressed. For completeness, I include referee 3’s report with this report, and I would encourage you to consider whether addressing any of the specific comments made would improve the final manuscript. However, as already noted above, my opinion is that the core of these criticisms has already been dealt with.

If you have any questions concerning these proposed actions, please feel free to contact me. Finally, I’d like to take this opportunity to thank you again for publishing in GMD.

Andrew Yool.

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Referee 3 report
 
I have read the paper and the author's responses to the reviewers' initial comments. My conclusion is that I agree with the reviewer who stated that "although the manuscript is well written, I feel that the content is more suitable for a technical report appearing on a modeling website, than a peer-reviewed publication in GMD." The manuscript seems to be an account of what an already-described model can do, but contains no clear research questions and thus no significant new information.

I also agree with the reviewer's comment that "the authors are essentially attempting to study 3D physical/biological shelf processes by ignoring advection. In many/ most shelf systems, advective processes play a critical role in controlling the distributions of nutrients and phytoplankton." Although I have used (and published) accounts of 1-D (z-t) models, and argued for the importance of 'vertical processes' in the short-term control of phytoplankton dynamics, I don't think it is possible to make reliable maps of biogeochemical processes in shelf seas using a grid of 1D models and without taking account of salinity. A specific concern is with the effect of lateral transports of freshwater buoyancy and nutrients, which are important in parts of the greater North and Celtic Seas, and I guess to be important in the east China Sea (e.g. the Chiangjiang plume).

Thus there is a scientific as well as a structural ground for recommending rejection. To end on a positive note, and to encourage the use of the S2P3 model in appropriate circumstances, the authors might consider publishing maps showing (e.g. for the NE European shelf) the magnitude of discrepancies between observed and simulated variables.

Thank you for your detailed and prompt responses to your referee comments. I am satisfied that the responses have addressed the comments raised. In particular, the manuscript is now much clearer on the utility of the model as well as the situations in which its use may not be appropriate.

I have not noticed any remaining issues to address, so recommend publication of this manuscript as is.