Dear Dr. Kodama and co-authors,

Your revised manuscript is now accepted for publication in Ocean Science. There are some technical comments, which I have listed below. Please prepare a final version of your manuscript accounting for these comments and corrections.

You are using data from other sources, e.g. GlobColour and AVISO. Please check the fair data use statements of those data providers whether the acknowledgement is correct.

I propose to use less abbreviations, like min S, or max T.

P1, L30-35 Please change to:
Ocean currents are important for zooplankton abundance and community structure: the Gulf Stream affects the abundance of copepods, Calanus finmarchicus and C. helgolandicus, in the European coastal seas (Frid and Huliselan, 1996; Reid et al., 2003), and the copepod species richness varies with the inflow of source water in the California current (Hooff and Peterson, 2006). Not only ocean currents, but also water temperature, nutrient supply, and many other factors affect zooplankton abundance and community structure; thus, monitoring results of zooplankton abundance and community usually reflect hydro-meteorological change (Beaugrand, 2005).

P2, L4-5 change to:
The TWC transport affects climate and marine systems in the Japan Sea and the Japanese Archipelago.

P2, L17-18 change to:
… but in two studies (Iguchi and Tsujimoto, 1997; Iguchi et al., 1999) heterogeneity in zooplankton community structure during spring bloom period was identified:

P3, L6 discarded (not: omitted)
P3, L7 Change to: As the temperature- and density-based definition of the depth of the mixed layer …
P3, L8 Japan (typo)
P3, L13 (from 6 to 19 hrs)

Section 2.1 Please provide precision and accuracy of the measurements.

P4, L27 remaining (not: remained)
P5, L6 clearly lower at (not: lowered to)
P5, L9 discharge (not: flow)
P7, L5, L6 diel (typo)

P7, L7-10 Change to (if my interpretation is correct):
Our consideration for rejecting the sampling time from the explained values was that the sampling was mostly done in the day-time (Fig. 2b), and the bottom depth is shallow in the western part of
our sampling site (Fig. 1). On the other hand, our results show the day-time zooplankton community structure: the variation of night-time may be different.

P7, L18-19 Change to (if my interpretation is correct): Although RD2 and RD3 only show a minor contribution to the spatial variation of zooplankton community structure, we attempted to interpret the data.

P7, L23 increases
P7, L28-30 Please modify this sentence, because it is not clear what is meant.
P8, L5 I think this should be: These affect the zooplankton community as well as temperature.

P8, L7-8 Change to: For example, in the Mediterranean Sea the river input changes the amount of phytoplankton, which in turn affects the amount of zooplankton (Espinasse et al., 2014).

P8, L11-12 “The results of RD1 were contained the bottom depth in the regression analysis, but the coefficient of bottom depth was significantly lower than the mean T (Table 2).” I do not understand this sentence exactly, please change it.

P8, L12-14 Change this sentence to: This indicated that the bottom depth did not directly contribute to the zooplankton community structure, although in other studies it was shown that the deep layer is the habitat of zooplankton which migrate to shallower depth (e.g. Herman et al., 1991).

P8, L30 delete: As the results
P8, L32 with (not: between)

P9, L5-7 Change to: We consider that the zooplankton abundance and community structure is generally not explained by “on-site” (in situ) environmental variations: large ocean systems can also influence the local zooplankton community variations, which is also observed in European seas.

P10, L12 I do not understand the use of reproducible here. Please explain and change.

References
Fernandez-Arcaya et al: no page numbers
Hirose et al 2009: please add doi for completeness of this kind of reference.
Legendre and Legendre: Please add city of publisher.
Nakada et al 2002: Japanese (typo)
Ohtsuka and Nishida: Japanese (typo)

Figure 1 Please indicate what the arrows exactly represent.
Figure 3 (counters) should be (colors), right?

Thank you and best wishes
Mario Hoppema