Dear Authors,

Your paper was reviewed by two referees who had an overall positive opinion on the paper but raised some items to improve and clarify. You have answered to these items in your responses. Thank you for that. Based on this discussion I think a minor revision is required to finalize the paper, in-line with the edits that you indicate in your response to the referees.

I specially encourage you to pay close attention to the following two statements of the referees:
1/ What general conclusions can be drawn from the analysis? Stress in the revised manuscript in which aspects your work and results have a meaning that goes beyond your application to the San Francisco Estuary and can be relevant for the other studies of similar systems.
2/ Discuss the context of your model application with regard to other possible approaches/models. Referee 2 indicated some other approaches and asked for more information which you provided in the response. Add this to the revised manuscript. Connected to this question is the issue of the dependence of the result on the network setup. Please make an effort to clarify these questions so that the generality and context of your approach/results becomes clearer.

I will ask the two referees for a quick review of your revised manuscript so they have a chance to judge how their comments/criticisms have been incorporated.

Best regards, Peter Molnar

The reviewers pointed to a lack of orientation of the paper. I think despite some good revising, there is still a lack of clarity in terms of what this paper is about in the introduction. Simply said, SSCs are important for the ecology of estuaries, but observations of SSCs are difficult to make, so we revert to coupled hydrodynamic-sediment transport models to make predictions at any place and time and conduct scenario analyses with them. This paper is an application of such a modelling, including calibration/validation tasks, etc., to a particular and important delta. A clear statement like this is missing in the introduction.

Page 1, Line 16: Please rephrase „…chain of models connecting models on contaminants…“

Page 1, Line 26: scenarios are plural?

Page 1, Line 27: Please replace the term „trustworthy“ with a more technical term, like reliable, accurate, etc (also page 19). Also the end of the sentence after the comma is disconnected.

Page 2, Lines 1-2: How is this rather unclear statement relevant for the abstract? The abstract should reflect your conclusions.

Page 3, Lines 7-9: Please do not form a single paragraph by one sentence.

Page 4, Lines 4-8: This paragraph is out of place in this location.

Background – I think it would be better to call this section „Study site and model“ or something similar.

Page 7, Line 27: I do not understand the use of the word „circumscription“ here

Page 7, Line 31: mesh in plural? Also this paragraph is somewhat repetitive, you already indicate above that the mesh is flexible.

Page 8, Line 3: Non-sensical first two sentences. Please correct.

Page 8, Lines 16-17: Be clear about the ranges of application of the equations tbte in equation 2.

Page 9, Line 8: Initial conditions SSC=0mg/l are not realistic, can you add here that the initial conditions quickly dissipate, or some other justification for this choice.

You make no reference to Fig 3 in the text.

Section 3: Please rename the section to indicate what this is, e.g. „Results“ or something else but not „The next 5 centuries“

Page 10, Line 27: You refer to w here (and later in the text), but settling velocity is ws in the equation on the previous page. Please correct.

Page 11, Lines 1-2: I disagree with your attribution of Beven’s phrase to your statement about a single mud fraction, I am pretty sure Keith would also object. It suffice to say that a single mud fraction reproduces more than 90% of the sediment budget. Also the reference to Beven on page 12, line 29, about the need for statistical analysis is unclear and irrelevant. Please remove this.

Page 11, Line 5: Please make exact reference here to the sensitivity metrics that gave you this best parameter set, do not be vague about this. What is tau_cr erosion or deposition, what is E? It is not a parameter in Equation 2. Please check and correct all parameters and equations.

Page 11: Please explain your “standard” run. I initially thought this was a best parameter set and now at this stage in the paper it is not clear anymore which is the best parameter set, and using which goodness-of-fit metric. Try to clarify this section please. Be aware that for most readers of HESS what you report as sensitivity analysis in Figures 5 and 6 is simply part of the calibration of a model. In Figures 5 and 6 explain the parameter symbols in the caption.

Page 11: You write twice in this section that getting a best fit at one station does not mean getting a best fit at another. That is trivial and does not need to be repeated. However please clarify in your paper that despite varying performance you are looking for one single best parameter set. I hope this is what you do...

Page 13, Line 14: You argue for the need to initialize the bed with a “concrete” bed, please rewrite this, you know there is no concrete, call it something else (also in Fig 9), e.g. fully immobile bed, or something like that. It appears best results are reached when the deposited sediment is compacted and not easily remobilized?

Figure 8: Did not reproduce correctly in the revised manuscript. Please check.

Figure 9: I do not see the black line you mention.

Page 16, Lines 28-29: What is Equation 6? In Equation 7 I do not get your angled brackets, if they represent the mean fluctuation, are they correctly placed? Please check.

Page 18, Lines 18-19: This sentence does not make sense.

Page 18, Lines 23-24: robust model for simulating sediment dynamics and budget?

Page 20, Lines 4-8: These are very clearly saying the advantage of the modelling. Reflect this statement in the abstract.

Page 20, Line 25: Where does the 90% accuracy come from? Make sure it is stated in this way in the text.

Page 1, Lines 26-28 in Abstract: the end of the sentence is incorrect grammar, you probably want to say something like "predictions and contain useful findings for..."

Page 8, Lines 9-11: Do not write this section as a note. If you really neglect the second term in Equation (1), then simply write Equation (1) as: D = ws*c*(1-tb/td) \approx ws*c, and in the text below write that in Equation (1) like Winterwerp (2206) you are assuming that deposition takes place regardless of the prevailing bed shear stress and td is considered much larger than tb.

Page 16, Line 23: Either put this equation on a separate line if you want it counted, or don't, but then renumber Equation 7.

Page 18, Line 12: I think you mean to say "the sedimentation process is gradual and steady"

Page 20, Line 19: wit h?

Page 23, Line 21: wrong citation

Page 34, Fig 3: You did not understand my comment. There is a Figure 3 in your paper, but you are not making any reference to it anywhere as far as I can find. So either delete the Figure or make reference to it.

Would it be possible for you to have a native English speaker read the text once to remove small grammar mistakes (articles, etc.)? I see one of your co-authors is from the US, this should be possible? Thank you.

Peter Molnar