Dear Dr. Lu and co-authors,

Thanks for the resubmission, which is much improved. This is certainly also due to the useful comments and critiques by the referees, in particular referee #3. Below are some comments which I encourage you to take into account.

There is one answer to referee #3 that is not clear to me. This needs additional clarification:
11. No information is given on initial conditions of the biogeochemical model. Without a sensitivity analysis, the statement that the ecosystem model is insensitive to initial conditions is not serious.
Your Answer: As we showed in Line 177: “The initial distribution of nutrients and dissolved organic matter was also interpolated from the WOA climatological data. Small values were analytically assigned to other ecosystem variables since the ecosystem module was less sensitive to the initial conditions of these variables. Some studies related with ecosystem modeling (Lu et al., 2015; Wang et al., 2013) was less sensitive to the initial condition (except for nutrients), which are cited here in Line 180.
Editor: It is still not clear to me what you’ve done. Why would you assign small values (if you don’t know them; and the reason you give I do not understand)

In the Data section (§2.1) some of the data used is presented, which is fine. However, in §2.3 Model Description, many additional data are mentioned. Please pull all data together in one section, §2.1.

L101 delete: geostrophic, as you wrote in the response that you would do (point 27 of referee 3)

L139-140 “Climatological river discharges from the Mekong River and other major rivers are included as point sources.” What is the origin of these data?

L146-148 This was added as a response to referee #3 (point 10). What would be the important issue here is, how would these other phytoplankton species change the results of the model? The manuscript needs a statement about this issue.

L148-150 “The CoSINE model was successfully applied in the study on the primary production (Liu and Chai, 2009), mesoscale eddy and its impacts (Guo et al., 2015), and the phytoplankton community structure (Ma et al., 2013, 2014) in the SCS.” What does this mean? How successful was the model and in what?

L154 “Small values were analytically assigned to other ecosystem variables …” Which variables are meant here?

The second paragraph of the Conclusions (“To further investigate…”) is like part of a summary. I suggest to shorten it and integrate it into the third paragraph.

With best wishes
Mario Hoppema

Dear Dr. Wenfang Lu and co-authors,

Your manuscript is now accepted for publication in Ocean Science. The only technical issue is the new citation, which should be cited in the text as:

Steeman-Nielsen and Jensen (1957)

and appear in the reference list as:

E. Steeman-Nielsen, E., and Jensen, E.A.: Primary oceanic production: the autotrophic production of organic matter in the oceans. Galathea Report, 1, 47-136, 1957.

Thanks and best wishes
Mario Hoppema