Dear Authors,
Thank you for your reply to the referees’ comments in the interactive discussion stage of the manuscript.

You have already signed that you intent to address most of the comments of the reviewers in the revised version. Please take into particular consideration, the instances when the reviewers raising questions, as these sections of the manuscript seem to be in need of further clarifications.


Overall, the work presented here is of relevance to the interdisciplinary scope of Earth System Dynamics (ESD) and the special issue to which the manuscript was submitted.

After taking into consideration the manuscript, the referee comments, your responses to the referees and my own editorial comments (for details please see below), the manuscript would benefit from a revision to clarify certain aspects and to further strengthen the document, particularly with regard to the interdisciplinary readership of this journal.

I look forward receiving the revised version of your manuscript that should incorporate the reviewers’ comments and the editorial remarks below.


With best wishes,
Julia Hall




General Comments:

In this manuscript, flooding is investigated with the focus on the flood generating mechanisms related to precipitation. As the ESD is a interdisciplinary journal I suggest that the authors add some additional information in the introduction on other possible flood generating mechanisms, but highlighting that are not being further investigated in this study.

In the entire manuscript, please adjust how the references in parentheses are given (i.e. instead of (Reference et al. (XXXX)) or (Reference (XXXX)) use (Reference et al., XXXX) and (Reference, XXXX) respectively. Please also see http://www.hydrology-and-earth-system-sciences.net/for_authors/manuscript_preparation.html ‘References’ for more details on referencing formats and for the ‘Examples for reference sorting’.

Throughout the manuscript, the authors introduce and describe new methods.
To make the workflow of the analysis clear to the reader, please compile all methods used in the study in one single methods section.
In the new methods section, I recommend that the authors describe their workflow in detail and how the individual analysis steps link together, as currently the train of thought is not clear.
Additionally, particular attention should be given to the physical reasoning behind the application of a specific method to scientific problem that is being addressed. The authors should communicate to the reader why the chosen method is applied in the current setting and what are the advantages, caveats, and limitations of the method in the current setting.

I think the manuscript would benefit if the results obtained would be discussed with a stronger focus on the physical interpretation and meaning.
This could be done, for example, in a separate discussion section in which the results would also be discussed in the setting of the broader literature.


Comments to Figures:

The manuscript contains several very interesting and informative Figures.
To maximise their readability and information transfer, I suggest the following changes to the Figures:
- Please use in all Figures that use spatial data the same geographical projections to allow for easier comparison and evaluation of the different Figures.
- Please make sure that all figures are also legible for someone who is colour blind (i.e. avoid the use of red and green colour in the same Figure). On this see also (http://www.earth-system-dynamics.net/for_authors/manuscript_preparation.html Point 7 under ‘Figure composition’. For example on the website http://colorbrewer2.org you can pick colour palettes that are ‘colour-blind safe’, or you might want to check your Figures using various online tools (for example: http://vischeck.com/vischeck/vischeckImage.php).
On this please also the http://www.earth-system-dynamics.net/for_authors/manuscript_preparation.html
- Additionally, when using the same colours in several different Figures (particularly if they are meant to be interpreted together), please make sure that the colour at the zero level is the same to allow for a meaningful comparison (e.g. by using diverging colour schemes).
-Finally, please check that all text used in the Figure remains legible when the Figures are being resized for the final publication (i.e. ~8cm for a single column Figure or ~18 cm for double column). E.g. in Figure 2 the size of the text and the numbers need to be increased together with thicker red line or in Fig 14 the line width and the size of the arrow head needs to be increased.

Figure 2: the colour scheme used in the right panel is not intuitive, which makes it difficult to determine if neurons 1 and 3 or neurons 2 and 4 have ‘smaller distances’. I suggest using a sequential colour scale instead.
Additionally, I suggest adding the neuron numbers into the blue hexagons in the right panel for ease of interpretation.

Figure 3: Please add labels to the rows (i.e. t-5, t-4 … t).

Figure 9: Please add a more detailed legend to Figure that shows either the point size of several percentages or at least the maximum %, 50% and the minimum %.

Figure 13 and 14: You might want to add the river network in the background of the Figure to allow for easier comparison.

Figure 15: I support the suggestion from Referee #2 to combine Figure 1 and 15. Maybe this can be done by adding the sub-basin outlines (without fill colour) and the numbers to Figure 1 as they appear in Figure 15.


Specific Comments:

In the introduction section, the authors use several times the term ‘exceptional floods’. Please add a definition of what this means in the context of the current manuscript.
P3L31: Please specify which of the two basins mentioned above the ‘It’ refers to.
P4L14: For the interdisciplinary readership of ESD, please provide more details on what the ‘naturalised’ streamflow data entails.
P4L23: For the interdisciplinary readership of ESD, please provide more details on the threshold selection of the empirical flood quantiles.
Additionally, please elaborate how the 70th percentile is in line with the interest on ‘exceptional floods’ stated in the introduction section?
P4L31-33: the procedure described here is not clear to me. Can you elaborate what ‘with respect to the day being evaluated’ means with regard to the ‘long term monthly mean’.
P5L11: On page 4 it is stated that ‘naturalized mean daily streamflow data is used. Here the authors now mention river stage as a means of defining a flood event. This might be confusing, consider rephrasing.
P6L3: What are ‘tuned parameters’?
P8L30-31: It is not clear to me, why ‘neuron 4 likely reflects conditions close to average’? Please elaborate further on this.
P9L10: ‘we do not expect substantial changes…’ Is this based on informed hypotheses or was this tested?
P11L1-2: the 11% given here are based on an original transition probability of 0.117 and the 35% are based on 0.347 as given in the Table 1. It seems that in both cases different rounding rules were used. Please check.
P11L8: Please elaborate why you have chosen to begin the transition cycle at neuron 3.
What is the physical reasoning behind this? Additionally, please highlight at this point in the paper again, that the neurons do most likely not transition.
P 11L16-24: For the interdisciplinary readership of ESD, please elaborate this aspect in more detail with physical explanations in mind.
P11L25-P12L18: For the interdisciplinary readership of ESD, please provide a more physical interpretation of the scaling results.
P12L6: Please specify what statistical test was used.
P12L7-L9: It is not clear to me, how from the analysis conducted one can make interpretations on the ‘rainfall intensity’. Please elaborate on this.
P13L24-P14L1: This sentence is not clear. Please consider rephrasing.
P13L21 & 14L2: Please consider rephrasing. The term ‘flood propagation’ suggest some sort of physical connection and downstream of the flood (i.e. being on the same river channel), which is not the case for all arrows. The same applies to the term ‘flow direction’ used in this paragraph and the Figure captions.
P14L5-L15: Please interpret the results more physically, linking the process interpretation to the results from the other sections. In your interpretation you might also want to discuss the time that a typical flood wave generated in the headwaters would need to travel to reach the basin outlet.
P14L7: Please specify, that you mean by ‘the largest synchronisation’. How is this quantified?
P 15L20: Please specify, that is meant by ‘spatial scaling exponents’ in this setting.

For the interdisciplinary readership, please make sure that you define all variables e.g. Q on page 13 or Q and A in Figure 11 and 12.

Dear authors,
Thank you for submitting the revised version of your manuscript.
In the revised version, the manuscript improved considerably, particularly with regard to the increased focus and better clarification on the mechanisms behind the observed phenomena.

Before the manuscript can be accepted for publication, please address the comments from referee #2 in the second round of review and also my comments listed below.
Additionally, please check again that you have addressed ALL comments from the first round of reviews. There are several points that were ‘promised to be corrected/amended’ in your response to the referees but were never incorporated into the final document.
I have detailed some of the points in my comments below but did not include all of the issues raised by the referees that have not been addressed in the current manuscript yet.

Specific Comments:
Generally, the word ‘somewhat’ is used very often in the manuscript. You might want to consider rephrasing for some instances.
P2 L14: Please specify which processes you are refereeing to.
P4 L17: I’m not sure if this reference is appropriate, as the reference given does not contain any information that would assist the reader with further information. I suggest giving the percentage of floods in this season instead. This has already been mentioned by one of the reviewers and it was ‘promised’ that this would be added but has not been added so far.
P5 L11-13. Please rephrase the sentence for clarity and check grammar.
P5 L17-22 Please add references to all general statements presented in this section.
P8 L1: Please quantify what ‘main rainy season’ entails and add reference for that statement.
P8 L6: ‘The understanding … will be qualitatively explored’. Please rephrase sentence, currently it reads as if the understanding is explored, which is confusing.
P9 L7-9: Please rephrase sentences. Currently the meaning of the sentence is not clear and/or the grammar seems not correct to me.
P9 L30: ‘neurons 3 and 4’ need to be replaced with ‘neurons 3 and 2’
P 10L3-L13: I think it would be beneficial to the reader if the description of the anomalies would focus more on the positive rainfall anomalies. E.g. for t-5 and t-4 for neuron 2 the rainfall field is not just ‘somewhat homogenous’ but appears to be a larger scale positive anomaly and the progression of negative rainfall anomalies (rainfall less than the long-term average) at later time steps seems to be of less importance for the flood generation. This applies similarly to the other neurons as well.
P10 L14-L17: This paragraph is somehow repetitive of the first paragraph on this page. I suggest combining the two. Additionally, when looking at Figure 2 I think the last sentence should read ‘The shortest distance is obtained between neurons 3 and 4, followed by the distances of neurons 2 and 4 and neurons 1 and 3’, to preserve the decreasing order of the distances.
P10 L28 – P11 L14 Please elaborate for the interdisciplinary readership of ESD that a negative divergence field (i.e. convergence) indicates that rainfall can occur (brief description of the processes involved), but please also make the reader aware that rainfall does not necessarily have to occur.
P11 L1: ‘negative events’ of what? Please elaborate.
P11 L2: ‘The SALLJ is weak’ it is not clear to me to which part of the text before this statement refers to. Please clarify.
P11 L9 For clarity, please add ‘positive’ before ‘divergence’.
P11 L11-13: ‘Neuron 4 has a moisture transport pattern somewhat similar to that of neuron 2, but the origin of the fluxes are more associated with the South Atlantic, with meridional fluxes west of the basin, and a less intense but still relatively homogeneous moisture convergence.’ From Fig. 4, I am not able to come to the conclusions that are written after the word ‘but’ in the above sentence. The two panels look very similar to me. Please check again and rephrase.
P11 L 15-27: Please add a sentence explaining to the interdisciplinary readership the reasons behind choosing to analyse the 850 and the 500 mb (i.e. what different type of conclusions can be drawn at the different levels).
P 11 L16 Please specify to the reader what kind of wave activity and what dynamic forcing you are refereeing to by better describing the mechanisms involved.
P 11 L23: The attribute ‘through’ only applies when specifically talking about a wave, however here it is used in connection with the word ‘circulation’. Please rephrase statement for added clarity (see also sentence describing neuron 3).
P 11 L24: Please be more specific where ‘southwestern of it’ is located (similar to how the location was described in detail for Figure 5)
P 11 L28 replace ‘is shown’ with ‘are shown’
P 12 L1: For clarity please specify the altitude, where the described ‘El Niño region’ is located and what definition of Nino is being used. This has already been mentioned by one of the reviewers before but has not been incorporated yet!
P 12 L5 please add ‘whether’ between ‘or’ and ‘they.
P 12 L8-10: What does ‘(3)’ refer to? Figure 3 ? Additionally please elaborate what ‘the results of Doyle and Barros (2002)’ were. And please also add the latitude location of the tropics and subtropics for ease of interpretation.
P 12L19: when rounding the number in Table 1 it is probably ‘17%’ and not ‘18%’.
P12 L 22: ‘neuron 4 (Fig. 3)’ should probably read ‘neuron 3’?
P 12L 24: The sequence should be 3 -> 1 -> 2 -> 4 -> 3. His has already been mentioned by one of the reviewers but has not been changed yet!
P13 L 7 I’m not sure if ‘remarkably’ is the correct term to use here. From all the analysis done before in the paper this does not seem to be ‘remarkable. Please rephrase.
P 13L19: Suggest replacing ‘average flow’ with ‘average flood flow’
P 14 L 6: Replace ‘the edges the …’ with the ‘the branches represent the….’
P 14 L 10-20 You might want to consider linking this also to Fig 3, by discussing the location of the areas with strong positive rainfall anomalies.
P15 L6 replace ‘peak’ with ‘peaks’?
P16 L 14: Please make sure that the link provided is working and that the link directs the reader directly to data source. Currently the link seems broken…


Figures:
Figure 1 please change colour scheme, as the red – green combination of colours will make it difficult to understand the Figure for people that are colour blind.
Figure 2: Please increase either the size of the red coloured numbers (both Figures same font size) or chose a different colour that has a better contrast with the grey surrounding, as currently the red numbers will be difficult to decipher once the Figure is scaled the correct size used for publication.
Figure 4-8: Please make sure that the 'zero' on Figs. 4-8 is the same colour (e.g. white), so the Figures are easily interpretable (i.e. it does not make sense that the zero line goes through the blue shading when a divergent colour scale is being used (e.g. in Fig. 4))
Additionally, to avoid confusion, please make sure that the colour code (i.e. red is negative & blue is positive) is the same for all of the above Figures (currently Fig 7 & 8 are the other way around).
Figure 4: Additional to the changes mentioned above, please provide a proper legend (with at least 3 arrows of different length) for the scale of the moisture fluxes, as currently one does not know how the arrows are scaled. Please also add to the Figure caption, that the arrows show the moisture fluxes and the colours the divergent field.
Figures 5,6,8 Please add the zero line.
Figure 13 & 14: The arrows are not visible, particularly in Fig 14. Please make them clearly visible (maybe a different colour for the arrow head or increasing the size of the arrow head might help).
Figure 14: You might want consider adding a box around the networks for clarity.
Additionally, once the Figure is scaled the correct size in the final publication, I suspect that the font used to identify the neurons might be too small. Please increase font size of the labels.

General Comment on References:
Please make sure that the references contain all necessary information and are written as outlined in: https://www.earth-system-dynamics.net/Copernicus_Publications_Reference_Types.pdf
Please make sure that all journal names are abbreviated according to the ISI Journal Title Abbreviations Index (https://www.library.caltech.edu/journal-title-abbreviations).
For example, ‘Journal of Hydrology’ should be written ‘J. Hydrol.’

The authors have satisfactory addressed the comments from the last round of reviews.
There are only a few corrections/comments before the paper can be accepted for publication.

General Comment:
Please make sure that either Parana or Paraná is used consistently in the text.

Detailed comments
P2L29: Please check the sentence, due to the correction in the last revision the sentence structure has become corrupted.
P4L16: ‘about 98 flood events (ranging from 76 to 131 events)’ This is not clear, is 98 the average for over all sites and the range is given per site? Please specify.
P4L 26: Add the values of ‘mb’ used for the low and high level vorticity.
P4L27: ‘It covers …. and are…’ Please correct sentence structure/grammar.
P5L 9 to 11: Please correct sentence structure/grammar.
P8L 7: Please specify what ‘m’ is.
P9L 25 to 28: The figure has changes since the last version, so now ‘left panel’ or ‘right panel’ should be replaced by ‘top’ or ‘bottom’ panel.
P9 L 29-30. Suggest swapping the order of ‘neurons 1 and 3‘ and ‘neurons 2 and 4’ to maintain the increasing order of distances.
P10L 11: ‘some connections’ Please specify/ elaborate.
P10L31: suggest adding ‘slightly’ before ‘positive’ or something similar to indicate that the southern part of the basin is not very positive.
P10L33: ‘also observed in …’ Yes, but in Fig 4 the dipole exists in the larger scale but not so much in Fig3.
P11L8-10: Please make sure that the sentence conveys that the values in the south have almost no positive values in the basin.
P11L10: ‘The moisture divergence pattern is again similar to the rainfall field at time t for neuron 3…’
I ‘m not able to see this. Please be more precise in describing what you mean.
P11L20: ‘also shows cyclonic rotation…’ the values in the Figure are very small, please indicate in text.
P11 L22-23: The trough is not only ‘weaker’ but appears to be very weak to almost non existing in the south of the basin. I suggest adjusting the language to convey this fact. (Maybe adding a zero line to the map in Fig 6 would help in interpreting this).
P11 L24: ‘centered around 45…’ Does this refer to the positive or the negative values. Please specify..
P11L26: ‘negative vorticity appears only in the south’ The negative values are very low and almost nonexistent. Please adjust text. And replace ‘kind of’ with a more specific statement (this also applies to P12L1)
P11L30: ‘also a sharp contrast’. Please adjust text, as the values are small and do not contrast shapely
P 11: Figure 7 is only covered by about 4 lines of text. I suggest elaborating a little more on the causes of the strong anomalies and sharp contrasts mentioned instead of just describing the Figure.
P12L 9: suggest either using ‘south of 40…’ or ‘around 50…’.
P12L13: ‘Combining all the analyses…’ Please specify which analyses are combined to reach the conclusions of the transition probabilities, as it seems that not all analyses are used.
P 24: Suggest making the red catchment boundaries in the inset map of Fig 1 thicker as they will be hardly visible when the Figure is adjusted to the smaller publication size.
P 25: Add to the Figure caption that the red numbers correspond to the number of the neuron.

Figures: Please correct the colour scale for Figure 3-4 and 6-7 to reflect a symmetric colour scale with similar linear increase for both negative and positive values.

References: Please remove/correct the several references containing ‘n/a-n/a’