This paper proposed a method for estimating river flow rate using a 3D flow model and field data. The objective is clear and important. However, the methods and composition of methods are quite common and practical, so a scientific novelty required for an original scientific paper is not enough in the present form.

I am afraid I misunderstand some details, but in my opinion, main scientific and engineering weaknesses of the hypothes of the manuscript are as follows:

1) Use of one rating curve for a channel consisting of a low-flow channel and floodplain (river engineers use two or more rating curves for such a river section better to explain the water level/flow rate relation)

2) Superiority of 3D model compared with 1D model sounds not fair (HEC-RAS had overestimated in Figure 9 for high flood but not sure how the 1D model was calibrated. In the Annex, it was said that the roughness was calibrated for high flow. If so, why was it overestimated in Figure 9? I think a 1D model can account for combined roughness parameters (not confident HEC-RAS can do, but accounting for the combined roughness of a compound channel with 1D flow model is standard.)

Point-to-point (mainly minor) comments:

L15: suggest adding 'multi-beam' before echo sounders (if you want to 

include single beam one, use parenthesis)

L17: hardware(s)?

L24: 'determine how .... methods' incomplete sentence?

L25: 'the' hydraulic model?

L29: Meaning of 'physics-based' should be defined in the abstract if use it in the abstract. (Of course, we can guess that author is thinking 3D flow modelling is physics-based, but 1D flow model can be said physics-bases since the shallow-water equations are based on the Navier-Stokes equations which is used for 3D flow model.)

L30: permanent -> stable or immobile (or some others?)  ('permanent' sounds something like (very rigid) bedrock but the target site seems sand bar) 

L34: 'is most promising to use' A bit vague and logical flow of the sentence is not clear.

L36: remove 'b' before 'hydraulic'

L44: 'implement' would come prior to 'validate'?

L45: flow rate would be one of the most important inputs for the flow model (maybe authors see the flow rate as output, but such standpoint is not explained yet).

L59: 'It is within this technological gap....' hard to read?

L65: 'The process of applying' -> 'Distributing and surveying'?

L81: The sentence seems incomplete?

L91: 'within' ->'for'  (not confident)

L92: 'a number of times until' -> 'with different flow rates'?

L99: Combining DEM (obtained by LiDAR or photogrammetrically) and bathymetry (obtained by echo-sounding) are quite common in river engineering, so maybe introducing not only authors' output but other works would be good.

L122, 'the 2 other sites' a bit vague? 'the two sites discussed in previous works (one or two citations)'?

L228: add 'software' before 'D-Flow Flexible...'?

L132: 'in thickness' -> 'their thickness'?

L162: 'point cloud' suddenly appeared.

L164: 'does not affect the water levels' is it realistic? (For subcritical, non-uniform, varied flow, local water level is affected by the downstream flow, I think. Of course, I understand what you want to say, but you can say it with different expressions)

L164: 'A small selection ... is taken' not clear.

L 186: 'the coordinates of known surface velocities' -> ' the surface velocity distribution'?

L 187: 'the coordinates of known water levels' -> ' the water level profile'?

L 190: better to show the equation of MAD for improve clarity (it's not strong suggestion but maybe help some readers to understand)

L202: 'iterations which estimated the water level based on slope' a bit vague, and better to explain more details. I think we can have results quite similar to the result of WARMA if the 'expert' do the iteration?

L222: Is this a sub-section title?

L232: '=/-' -> '+/\'?

Does the table necessary? (Surface velocity seems to be used for both calibration and validation, it's good if there is some discussion about it)

Table 2: How were the distribution and sample size of three properties discussed in the table? (the result of current metre shows no minimum. Is this show the problem of the current metre survey? (it's hard comment so able to skip))

L261: A bit difficult to understand how this conclusion can be obtained from table 2. (LSPIV shows the minimum with 0.015 s/m^(1/3) but why choose 0.013 as a conclusion)

L273: remove 'of' at '100 m3/s of were'?

L274: 'four rating curves derived from D4DFM; one based on....' Misleading? (two rating curves were based on D4DFM but two others were not?)

L299: Spell out 'OLS'?

L299: P_{bias} and E_{ns}: compared with 17GCPs result or WARMA? (maybe with 17GCPs but better to indicate(

L314: Better to indicate the reference if the uncertainty used here (also for L329)

L323: 'more stable roughness coefficient' a bit unclear.

L326: 'schematized' and 'schematization' are used very close, maybe can be rephrase to improve readability.

L342: figure(s)?

Bibliography of Kim. Y (2006) could be edited.

Figure 9: Labels 'measurements HEC-RAS, D3DFM, Combined roughness' are a bit confusing. something like'estimate with HEC-RAS, D3DFM (single roughness), D4DFM (combined roughness)'?

Figure 10: The regression line seems weighted to high flow. Is there any reason? (based on annex B, it seems logs are applied to both axes)

Figure 13: It's just my interest, but it's better to add the data points of 1200 and 1400 m3/s, and I want to see if there are some disconnections in the relation, like Figure 12.

That's all.

The study focuses on the use of cutting-edge technology to estimate river discharge. Although the methods and results are interesting, the research fails to clearly explain the contribution to science. The advantage of using this UAV-system vs traditional methods is not clear. These traditional methods are cheaper and therefore more affordable compared with the described systems (i.e., drone, GNS, eco sounder, etc). However, traditional methods are based on point measurements and heterogeneity of the river geometry is not contemplated. In contrast it seems that the UAV-system can capture the spatial variability of the channel shape, hence probably a more accurate flow discharge.

I would recommend refocussing the problem statement showing scientific evidence of how point measurements fail to estimate river discharge. There is a hint of this during the introduction (e.g., L68 and L74) but is not addressed very clearly. For instance this should be emphasised in the abstract - perhaps it can be the opening sentence. Also, in the introduction, it would be good to show studies on the implication of different spatial resolution for the estimation of river discharge (use of Lidar and satellite data for river geometry, and gauging stations). It will also be interesting to show the spatial resolution of your UAV-system. How does this compare with the available DEM data (e.g., Lidar, satellite,  cm vs m)?

In general, there is a lack of discussion in the document. For example, you should discuss that comparing your method against traditional ones provides some sort of validation, and in fact as mentioned, more measures are needed for the reliability of your method. Also, it would be important to address in the discussion the differences between using a 1D model vs a 3D model in your results. Additionally, I believe that more than one rating curve should be used. Regardless of this, you need to discuss the implications of only using one rating curve.

I consider this research has substantial scientific merits. However, you need to improve the structure and the writing to make it more fluent and easier to read. I encourage to use the below suggestions and comments for an improvement. If the suggestions are not appropriate to the scope of the research, please reconsider better wording to transmit the idea.

Please find below specific comments.

L17 – What do you mean with “hardware”? Would it not be better to use the word “system” Also, the sentence “In short, the hardware can be used to produce the geometry” is confusing. Do you mean river geometry? The sentence, as it is, seeming to be incomplete or somehow needs to be related to the previous sentence or the following one.

L22- I recommend mentioning the novelty/contribution in the abstract. This can be place before objectives and after briefly explaining the problem.

L24 – Instead of using semicolon, I would recommend alphabetic numerating of the objectives (a, b, c, etc). This will allow the reader to easily differentiate between them.

L32 –Using the number 9 in parentheses is confusing, it only makes sense when reading the methods in the paper. I recommend removing it and leaving the sentence "beyond an optimal number" or change it to "beyond an optimal threshold of 9 GCPs".

L36 – remove “d”.

L44 – I would use the word “estimation” rather than “monitoring”. Monitoring can be confused with sensing, then it is better to clarify that models are useful tools for prediction rather than monitoring/sensing.

L45 – Use the word “apply” rather than “implement”.

L75 – I would remove the word "robust". It could be argued that more measurements and rating curves are needed to make the method robust. I leave it for your consideration.

L80 – Research questions are objectives rewritten as questions. Although, there is nothing wrong with this, it is repeated information. If the authors want to leave the research questions, I suggest modifying them. I leave it for your consideration.

L86 to L95 – It is not easy to follow the steps as they are written. I suggest numerating them (i, ii, etc).

L119 - Were the measurements of flow and water level contemporary with those of GCP and bathymetry? If so, what year was it (2022)? Could you please add in a table the data collection date, or maybe add this in table 1.

L210 – Add name of variables (O = observation, P, x, etc)

L222 – Seems incomplete.

L237 – Results should be section “3”. Previous section is “2 Material and Methods”.

L312 – I don’t recall you mentioning satellite data in the “2 Material and Methods” section. You need to add this in section “2.7”?

L353 -Where is the “discussion” section? I consider it very important to discuss the differences of using a 3D model vs the 1D model. Also, the use of more than one rating curve (if using only one discuss why?). The advantages of your method over others, etc

Figure 2 and Figure 5 - Legend and scales need to be bigger. It is difficult to read.

Figure 3 – I don’t think this figure provides important information. I would remove it also because it does not follow the same format as other figures.

Figure 4. – Subfigures require identification (a & b) and a respective legend. Also, they look identical to me. Make evident the “volumised and cut on both sides”. What do the colours mean? -depth (m)? Add a colour bar.

Figure 5 – I think figure 4 and figure 5 can be a single one (a, b, and c).

Figure 6- Use identification for subfigures (a, b, c, etc) and add their respective legend (5 GCP, 9 GCP, etc).

Figure 7 – Bigger legend.

Figure 8 – This is a good example of a figure.

In general, in the text there is a discrepancy in the format. Sometimes you use a space between new lines (L135, L160, L180, etc), sometimes you don't (e.g., L50, L59, L114, etc). Also, there are tabs where they shouldn't be (L221 and L214). In terms of the figures, you use different colour and letter sizes (e.g., Figure 1 a, b labels in black vs figure 2 a, b labels in parentheses and in orange).