Comments can be found in the attached document 

Please find the comments in the attachment.

This is a valuable manuscript that helps to gain insight on salt transport processes in well-mixed estuaries, such as the Guadalquivir estuary. The effects on salt distribution due to natural and anthropogenic freshwater outtakes from the estuary  is addressed. The topic is relevant as higher salt intrusion in estuaries is expected in the actual global warming and freshwater supply reduction context. 

My overall impression is positive, although the manuscript requieres a major revision before I could recommend publication. 

My major concerns are regarding the usage of terms, discrepancies between model output and observations, and citations. Please see specific comments below.

- I think that not all the discrepancies should be attributed to withdrawals. Evaporation rates could be particularly important during the dry season.

- If not considered, uncorrected phase lags (which are related to those of the tides) in modeled and observed salinity  yield also deviations. As the oceanographic vessel travelled upstream (How much time took the vessel to complete one survey?), the tide propagates and at different locations of the estuary the moment of the tide is different. I think the authors didn't mention whether along-channel modeled salinity is plotted at a given simulation time or at the time the salinity measurement was taken at each location.  The authors should discuss that. 

- Regarding terms usage, some of the them are inappropriate (salt wedge/front) for this estuary during low riverflows. Besides, higher/Lower salt intrusions do not occur at maximum flood/ebb.

- Please check references out, too. I think a few of them are not appropriate or out of place. 

Specific comments:

Abstract

L13. advection and dispersion module (there exists advective and diffusive transport)

L15. I agree with one of the other reviewers. There is no salt wedge or salt front in the GRE during low riverflows. Please use salt intrusion or saline intrusion. Salt wedge typically occurs in highly stratified estuaries. Change here and elsewhere. Salt front may form after high freshwater discharges near the mouth.

L17. Water withdrawal or sink term or outflow?

Introduction

L28. Perhaps Miranda et al. 2017 is much more “physical” than “biological”. I suggest to change citation here.

L29. + freshwater discharge + tides + wind

L32. I think is better here to cite a general reference on ecological systems better than Donázar-Aramendía et al., (2019), which is somehow more “local”.

L37. Remove Pritchard (not on the GRE) and Losada citations. If you want to include some here, I suggest Álvarez et al. 2001 or Díez-Minguito et al., 2013.

L39. Remove Reyes-Merlo et al. citation. The credit on this should go to Álvarez el al. 2001, I think.

L41. Remove citation. Citation here (Contreras and Polo, 2012) is on the influence of basin hydrology on the GRE. Please check out that statements throughout the manuscript are correctly cited.

L50. ‘and decreasing saline intrusion.’

Figure1. Xo is the landward limit of the model. Does the boundary condition of salinity at Xo vary with time?

L60. Bermudez et al. 2021 is on microplastic distribution in the GRE. I suggest to remove from here.

L62. ‘requires large amounts of freshwater’ ?

L65. Notice that none of the citations in on degradation of the ecosystem. Moreover, Zarzuelo et al. 2017 is a study developed in Cadiz Bay.

L79. And downstream, too. Seaward from Bonanza, salinity does not change so much either. Typically is modelled as a tanh(x) function. Nevertheless, it is possible that authors’ model domain leaves out this part of the salinity distribution.  

L86. -1 superscript.

L87. Climatic forcings

L89. Salt/saline intrusion

L92. Notice also that hydrodynamic model by Siles-Ajamil et al. is linear. Authors’ model is non-linear, which is quite an improvement.

L92. How does compare authors’ model with that by Bouke et al. (2022)? (https://doi.org/10.1029/2022JC018669)

Methodology

L121. Is really the focus of the manuscript the calibration and validation of the model? I think calibration and validation is necessary, but shouldn’t be the solely objective of the study. I suggest to rephase the sentence.

L123. Ok

L125. I suggest to mention or present these issues already in the introduction. It will help to motivate the object and give the proper context to the readers.

L130. ‘…along the estuary.’

Table 1. Salinity measurements along the estuary are not simultaneous. They are out of phase from one point to another point within the estuary (salinity changes locally during floods, ebbs, etc.). Are the different phases somehow corrected to present ‘simultaneous’ salinity values along the estuary?  (Also in L200)

After Equation (2) ‘.’ not ‘,’.

L148. Forces per unit mass.

L149. Units. Separate m from s

L150. Bottom friction or bottom drag coefficient?

L161. Why not include El Gergal and Brazo de la Torre too?

L170. Salt transport. Check out here and elsewhere: advection and dispersion transport (there exists advective and diffusive transport)

Equation (3). No sink terms in this equation? Could evaporation rates be comparable or may affect \delta estimates?

L197. Please, indicate determination coefficient of the fit and/or other performance scores of the calibration. (Or refer to Table 2)

Results and Discussion

L110-115. I think this must be better justified here or elsewhere. Authors must be clear how they drew the conclusion that there must be water withdrawals (although certainly possible). ‘Flow data by official sources?’ Do you mean freshwater discharges? What were the tidal and riverflow conditions?

F233. Please indicate if Figure 2 include the profiles with the sink correction. If not, it would be helpful to see also the uncorrected profiles.

Figure 2. Name the panels a), b) etc. to link better to what it is described in the main text.

L248-249. Please explain this according to the spatio-temporal variability of water extraction for agricultural activities.

L249. November 2023. Which panel?

L250. Could the authors provide a water volume to provide evidence for this? (Ok. Seen answer in L276)

L276. I understand that these water outtakes for crops could be difficult to obtain. However, could be estimated with authors’ model results.

L276-L282. Again. Explain whether or not the timing of the salinity measurements along-estuary and model output yields discrepancies. Also in L291 Figure 3), please indicate whether or not the model output along-estuary is plotted at the same time? I presume that the results obtained from measurements are not, since they are measured as the vessel travelled upstream. Discrepancies up to 10psu could be observed, depending on the location and timing.

Figure 3. Label is wrong in panel (e) (it says (d))

L303. What would be the increase of freshwater discharges from the dam in that case?

L315. Does the model need any spin up time?

L325. Theoretically, maximum (minimum) salinity values occur at high (low) water slacks, which occur at different times along the estuary.

Figure 4. Panels b) and c). Around km 17, along-channel salinity inversions are observed (larger salinity values upstream). Do have the authors any clue on this? Is due to tidal trapping in Brazo del Oeste?

L327. “the wedge demonstrates minimal intrusion”. Rephrase

L338-340. As the authors mention, saline intrusion is important for water quality and residence times are relatively large in the estuary. Nevertheless, notice that author’s model is cross-sectionally-averaged. This is ok, since mixing rates within the estuary are quite high. But should be recognized that the model does not resolve the vertical segregation of the flow, which could be important in the lower part of the estuary and enhance flushing times there.

L341. I don’t see how this conclusion is drawn. Please explain why there is a positive mass balance at the mouth? Is this due to evaporation rates or outtakes for crops within the estuary? Does this volume compensate for freshwater losses within the estuary?

Discussion of… (discussion in Section 3 and also in Section 4?)

I find this part the most interesting. Please consider to include it in Section 3.

L347-351. Perhaps the most recent estimates of salt intrusion trends in European estuaries are those by Lee et al. (2024) https://doi.org/10.1038/s43247-024-01225-w

L374. Yearly-averaged value?

L375-385. Maximum and minimum saline intrusion occur at slacks, not at maximum flood and ebb. I don’t think this alters authors’ point, but please amend here and elsewhere, and modify figures if needed.

L410-413 (here, before and after) I suggest to name the cases, including the reference one, and use the same notation in the Figures.

L421. (here, before and after). What E and F stand for? I suggest to change the names or not saying that they correspond with the minimum or maximum intrusion.

Figure 6b and 6d. The estuary becomes ‘inverse’, with higher salinities than at the mouth.

Conclusions

L452-455. I don’t think these (plausible) impacts are conclusions of the present work.

L461-464. That depends on the discharge released from the dam during high riverflow conditions. Freshwater discharges of about 100-200m3/s move off the salt intrusion to the estuary mouth but tides are only significantly damped on the upper part of the estuary. Discharges of one order of magnitude higher damp significantly tides all along the estuary.