The comments to the MS by Madkaiker et al are presented in the attached PDF file.

This is a very well-documented and very well-written paper. It concerns the application of a high-resolution model in the Northern Indian Ocean (NIO) with the view of revealing important patterns of the volume, salt, and heat transport under the prevailing climatological conditions. Apart from the direct outcome of this application, it also provides a quite interesting comparison with the findings of other numerical models in the region and available real-life datasets which is important and an asset of the paper. As a result, a pragmatic picture and features of the existing circulation and local physical phenomena are produced, most of which agree at a considerable degree with those described and analyzed by other researchers as well. 

A general comment though is that the paper omits a discussion section but incorporates it instead in the results. Given that the authors devote little space on the affiliation and contribution of their results to the environmental problems of the NIO region (e.g., ecological, and biological processes, nutrient and carbon transport, fisheries etc.), I would recommend adding a separate section and elaborate more on the matter, so that the scientific contribution of this paper’s findings to real life problems can be better stressed.

Other than that, only some minor comments follow:

Line 59  ‘augmenting its physical model to extend to various biogeochemical processes’ This doesn’t read very well because this is a numerical model that implements the laws of physics but does not involve any physical modelling. Please rephrase.

Line 72 INC-HYC is only explained in section 2.1.2 and line 124 but the acronym needs to be determined here.

Line 85 Please rephrase to ‘this study aims further to help’

Line 88 This sentence sounds like a phrasal error. Please rewrite it.

Line 94 Refer to  “Fig. 1 ”  inside the parentheses

 Line 123 what do you mean by simulated? The model is run, built or setup at INCOIS?

Line 131 ETOPO-1 acronym is not explained.

Line 139 NRL-HYCOM, INCOIS-GODAS. Please explain acronyms NRL and GODAS.

Line 515 similar comment to that for line 59 regarding the use of the term ‘physical model’

Figure 1. The purple color does not work well in contrast to the red symbols. Change the color for the ADCP locations so that they can be better distinguished.  There is a purple symbol missing from the Sri Lanka transect. Remove the brackets (in color scale). Please indicate where is AS and where BoB on the map.

Figure 5 Add units in the stick plots.