General Comments

This well written and thorough manuscript describes the biogeochemical processes occurring in the Elbe river estuary and links these to anthropogenic influences. The modelled biogeochemical cycles are well considered and describe a large source of TA within the estuary. This TA source is described as being caused by the dissolution of CaCO3 sediments which is assumed to be driven by the increased organic matter and N loading of the estuary. Biogeochemical processes are explored in detail, although much of this is hypothetical discussion.

One weakness of the study is that all biogeochemical processes are estimated from dissolved concentrations rather than from other field observations, for example benthic sediment incubations or water profiles.  The estimation of biogeochemical processes within estuaries is complex due to the dynamic interactions occurring over tidal cycles (salt wedge and tidal movements influencing benthic sediment interactions), diel cycles (changes is benthic O2 caused by respiration/photosynthesis), seasonal cycles influencing metabolism rates, and all influenced by different riverine flow rates. While I agree that the processes identified here are likely occurring within the estuary, the accuracy of the predictions (e.g. that 90% of TA is due to CaCO3 dissolution) may have a high level of inaccuracy and may have high temporal variability. It is useful to use modelled results, however it is important to highlight the uncertainties and assumptions associated with them in all sections of the manuscript.   

Other Comments

L17 – wording - ‘resulting in maximum’

L60 – I suggest separating the two research questions for clarity. I also note that the 2^nd research question doesn’t receive much attention in the abstract or conclusion.

L65 – Provide more detail on ‘surface water samples’.

L139 – What is the source of wind speed measurement DWD? If wind speed was not measured in situ then where was the data source and at what resolution was the data collected as wind speed can greatly influence flux estimates and this uncertainty should be clarified.

L157 – Provide details of box volume measurements and fill time estimates. Errors associated with both volume and fill time should be incorporated into the mass balance calculations. E.g. errors in the generic river width, depth etc. in Table 1.

L176 – Outer boundary conditions measured two months later. Is this an issue? Please justify.

L190 – The sentence is vague and poorly structured. Clarify the term ‘imported’ and clarify the link between PIC and CaCO3 dissolution.

L308 – This section contains the most clear findings of the paper but seems hidden within the manuscript.

Table 3. Errors of species in the first half of the table seem optimistically low. Are all cumulative errors considered? Errors of samples, box volumes, flow rates, fluxes…etc.

L437 – replace ‘vanishing’ with a more appropriate term.

L442-L447 – This speculation reads as discussion not conclusions

END OF COMMENTS

General Comments

First, I would like to congratulate the authors on a very interesting manuscript. It provides insight into the biogeochemistry of the described estuary and attempts to quantify contributions of alkalinity from various sources.

I have a couple general comments about this manuscript. Firstly, I would like to suggest that the authors have the manuscript thoroughly proof-read before publication. I found several grammatical issues and a general lack of flow due to sentence/paragraph structure throughout the manuscript. In the section below I have identified some of these. This should be addressed for the reader’s benefit.

Next, I have a general comment about the methods section. I think the authors should consider restructuring this section. First, a detailed description of the study site should be presented. I found that the authors did not go into enough detail when describing the estuary and it would really help “set the scene” for the reader if they bulked this up a bit. Sampling protocols should be removed from the study site section and have its own section that follows that describes the water sampling techniques as well as how each individual parameter was subsampled and preserved. The model/make of the CTD + O2 probe on the FerryBox should also be provided. I noticed that the authors have grouped sampling/preservation techniques in with each analytical procedure. These should be removed and added to the new sampling section above to make the process of the study easier to follow sequentially. Try the following structure for the methods: Study Site -> Sampling -> Analytical Procedures…etc.

My final comment very similar to that of Reviewer 1. The processes described in this manuscript are based on estimations instead of field observation. On top of that, the dynamic nature of estuaries can lead to high variability both spatially and temporally which adds large uncertainties to estimations from models. Although the conclusions presented by the authors are compelling, they should add a note in the discussion or conclusions stating that these estimations may be serendipitous due to large levels of uncertainty.

Other Comments

L31: Add Gilbert et al. 2005 (https://doi.org/10.4319/lo.2005.50.5.1654) as a reference when describing oxygen deficits. It gives a 72-year record of oxygen depletion in the St. Lawrence Estuary.  

L34: Grammatical error – “It encompassing an area that begins” should read “It encompasses an area that begins”.

L39-41: The following piece of writing does not flow well: “Eutrophication can cause large phytoplankton blooms both in rivers and in the coastal zone. Whose decay increases oxygen consumption….”. These few lines should be re-written to read something like the following “Eutrophication can generate phytoplankton blooms in both rivers and the coastal zone. This increased flux in organic matter can lead to higher rates of oxygen consumption which can drive hypoxia in stratified bodies of water such as estuaries and the coastal ocean”.

L41-42: When describing hypoxia in the coastal ocean you should add the following sources: Gilbert et al. 2005 (https://doi.org/10.4319/lo.2005.50.5.1654), Rabailas et al. 2001 (https://doi.org/10.2134/jeq2001.302320x), and Rabailas et al. 2002 (https://doi.org/10.1146/annurev.ecolsys.33.010802.150513).

L42-44: Again, there are some issues with flow here. Instead of describing the dredging then having a very short sentence with a statement that organic matter turnover exists, you should combine the sentences. Try something like: A hotspot of organic matter turnover exists upstream of the Port of Hamburg, where recently the sea floor has been dredged (increasing the depth from ~5 m to ~20 m) to increase accessibility for ships.”

L57-60: I agree with Reviewer 1 on this section. The goals of this study should be separated for clarity. Also, the authors may want to consider removing the use of first person identifiers such as “We” or “I” in the manuscript and opt for a third person approach. For example changing “We want to answer the questions of….” to “This study aims to answer the questions of…”.

L65: Grammatical error – “This study based on samples….” should read “This study is based on samples…”.

L155-157: Please provide individual box volumes and fill times.