We thank the reviewer for their constructive and helpful review of our paper. In following, we will reply to the individual comments. Reviewer comments are written in italics, our answers are kept in plain font.

I was a bit confused when the methods section talked about FerryBox sampling (Line 92) and equilibrator measurements of nitrous oxide (Line 132), yet the datasets only show discrete samples for the sampling stations along the 100 km transect (Figure 2). To be clear, I like the data presentation in Figure 2 because its clear and easy to follow, but at the moment the Methods section highlights sampling that is not reflected in the results section.

We agree that the current presentation of the FerryBox and nitrous oxide data does not represent the continuous measurements during our campaigns. For nitrous oxide, we will change the figure by plotting data points for 1 min averages along the transect. For clarity, we decided to keep the current way of presentation for the FerryBox data (salinity and oxygen concentration) with plotting only data points for our 20 min sampling interval. In the revised manuscript version, we will clearly refer to the fact that the plot only shows discrete points of the continuous measurement to avoid confusion.

The only continual measurements are a snapshot of dissolved oxygen concentrations over a 2-3 day period for fixed locations (Figure 3). Also, Figure 3 is less easier to follow than the other figures in the manuscript and I think future readers would appreciate efforts to make it more interpretable.

We will modify the figure caption by adding a brief sentence on sampling points, i.e.: "In 2014, oxygen concentration was measured at two sampling stations at stream kilometers 11.8 and 24.5. In 2020, additional measurements were done at stream kilometers 18.2 and 33.0." We will further evaluate changes of the figure that may improve clarity.

It wasn’t clear to me whether the authors interpret the datasets obtained six years apart (in 2014 and 2020) to be sufficiently similar that they can be considered a sampling replicate or whether there are differences between 2014 and 2020 that indicate changes to the N cycling. Looking at Figure 2, there appear to be differences in nitrite concentrations and also the isotopic composition of nitrate. Is this noteworthy to the readers? Discussion of this could be included when discussing differences in the PCA plots on Figure 5?

Thanks to the referee for the comment. We interpret the data of both sampling campaigns not as sampling replicates, but as sufficiently similar for comparison to evaluate the zonation of the estuary. With a six-year time difference, we cannot ensure identical sampling and measuring conditions for both cruises that would be necessary for true replicates. The PCA analysis showed that nitrogen turnover was comparable in both years. However, there are distinct differences (such as the occurrence of assimilation in the outer estuary, which is much more distinct in 2020) between the cruises that we tried to address in the manuscript.

Seasonal and interannual variation may cause differences in dissolved inorganic nitrogen distribution and nitrate stable isotope composition. Water temperature and discharge were significantly higher during our cruise in 2014 than in 2020. The offset of nitrate isotopes fits relatively well with the observed shift of salinity, oxygen and ammonium concentration. In the manuscript, we argue that these shifts may be driven by the increased discharge (Line 285 - 290). The increased nitrite concentration in 2014 may be caused by enhanced temperature that fuels microbial turnover.

In general, we see the same nitrogen turnover processes along Ems estuary during both cruises. There is no evidence hinting significant changes that were not caused by seasonal or single effects. The PCA independently confirms the same zones of nitrogen turnover for each year. The loadings of the principle components were also similar for both cruises.  

In summary, the two cruises allow a more robust assessment of general N-cycling patterns in the Ems than a single campaign would, but they can certainly not be regarded as replicates. We will briefly address similarities and differences in the revised manuscript where we see fit, most likely in the section addressing the PCA results, as suggested by the reviewer.

Line 362 The authors justify using an isotope effect of 10 ‰ based on unpublished data. This is should be changed. The authors can always deposit the data in a free public database e.g. zenodo, and cite the doi.

The data was presented at the EGU in 2014 (Sanders, T.; Daehnke, K.: N-Isotope fractionation of nitrification in the tidal influenced Elbe River estuary, Germany. In: European Geosciences Union General Assembly, EGU 2014. Wien (A), 27.04.-02.05.2014, 2014.). We will include the conference abstract with its doi as a reference. In addition, we are currently working on a publication of the data as a short communication. Inclusion of the data in a data base is difficult, as these are results from incubation experiments that needs further method explanation, and this format not easily included in a free public database like, e.g., PANGAEA.

Line 443 ‘Furthermore, our results as well as those from 1997 were obtained from a single survey in June making the comparison intruding’  This is just a small language error, the authors should change intruding to intriguing or another word to better reflect their intention.

Thanks for the comment! We will correct this to intriguing in the revised version.

Figure 1. Is it possible for the authors to either indicate on the map, the four sections that are referred to in the text, or draw a transect below the map that indicates the four zones?

We will include indications for the four sections in a new version of our map.

Was the O2 sensor data included in the Supplementary Material? I don’t think I saw it there.

The oxygen data is not part of the supplement materials. We did not include it, because we used data provided by the German Federal Institute of Hydrology (Bundesanstalt für Gewässerkunde – BfG). The BfG itself plans the publication of the data soon in “BfG-Report No. 2077”. As soon as the report is published, we will provide links to the data. We hope this is sufficient, as all measured data points were presented in the figures 3 and S1.

We thank the reviewer for their constructive and helpful comments and suggestions about our paper. In the following paragraphs, we will reply to the individual comments. The reviewer comments are written in bold italics, our answers are kept in plain font.

This paper presents an interesting and detailed study on the inorganic nitrogen dynamics in a hyperturbid estuary. The study is original as it combines a classical biogeochemical approach based on concentration vs salinity profiles with an in-depth use of isotopic data. Overall, the authors use a quite complex method to estimate nitrate transformation amounts (denitrification and nitrification) based on isotope data for different zones. However the authors do not compare these values to the overall nitrate concentration in the estuary. In other words, are the observed processes significant or not at the scale of the estuary? And is the estuary, as a whole, a net source or sink for nitrate? If I’m correct, production/consumption quantities estimated by the mapping approach are quite small compared to the NO3 concentration: a net overall consumption of 9 µM (-16 + 7 µM) in 2014 and a net 0 in 2020 (-10+10 µM) for zone 1 and 2 together. When compared to the initial 150-160 µM of nitrate, transformations are small or even unsignificant. For this, I could suggest to complete the analyses based on isotopes with a more classical nitrate mass balance approach.

First, we want to thank the reviewer for the comment. A mass-balance approach, as suggested, is certainly valuable. We do unfortunately not have the data to perform an adequate mass balance calculation, as this would require either areal process rates, or residual flow into the North Sea at the mouth of the estuary. In a tidal estuary, such flow measurements are difficult to obtain, the effects of changing tides and residence times must be considered, which actually would require a demanding modelling exercise that alone could represent another publication. We do fully agree that a detailed mass balance is a worthwhile approach, which should be followed up on in the future. Potentially, this can be done by extrapolating areal (or volumetric) process rates, similarly to Deek et al (2013).

However, our intention was to investigate the effects of biogeochemistry and morphology on individual turnover processes (e.g., denitrification/nitrification). A detailed mass-balance is beyond the scope of our study.

We do agree, though, that our data do actually not allow solid conclusions on the overall source or sink role of the estuary. We will remove these statements in a revised version and refer to source or sink functions of individual sections of the estuary. In these sections, we do see significant net deviations in comparison to conservative mixing, which naturally will affect the overall input if their activity ceases.

L13 – precise “their morphology have been changes” in accordance with the type of changes you cite. Other type of change – like chemical or biological changes have also occurred.

We will specify that morphology has changed, following to the suggestion of the reviewer.

L32-32: Maybe precise you focus on morphological change here. Other types of changes may also arrise such as wastewater treatment in the basin or fertilizer regulation, etc...  like you write later.

We will specify that we are referring to changes in morphology in this text passage.

L56: what do you mean by “properties”?

L61: what do you mean by “properties”? be more precise

L65: idem

We refer to biogeochemical properties that we measured during our cruises. This includes the nutrients, oxygen and suspended particulate matter concentrations as well as discharge conditions, water temperature and pH. We will specify the water column properties we refer to in the introduction chapter to be more precise.

L58: precise that both are summer cruises

In line with the suggestion of the reviewer, we will clarify that both cruises were done in summer. Further, the months of our sampling campaigns are specified in the chapter “2.2 Sampling”.

L59: is it not also highly urbanized? – so high population density?

The catchment of the Ems River is rather characterized by agriculture und land use area than by high population density. Agricultural land-use is dominant in the catchment (80%), whereas urban land use makes up for 8 % of the catchment (FGG Ems, 2015).

L71: Can you mention the population density? This info is always interesting when comparing watersheds with each other.

We thank the referee for the suggestion to add information about the population density. We will add the population density of ~200 km^-2 (UBA, n.d.) in the study site description.

L60: increased SPM: compared to what? Previous years? When did this start?

The suspended particulate matter concentration in the Ems estuary increased compared to values measured before deepening and dredging activities in the estuary. De Jonge et al. (2014) found a 2- to 3-fold increase of suspended particulate matter concentration in the lower reaches of the estuary in the timeframe from 1954 to 2005. In the Tidal River even a 10-fold increase was observed. We will specify in our text that it is a comparison over time. Further, we will add information about the timeframe and magnitude of the increase that we refer to in the comparison.

Figure 1: Locate the Dollar reach on this map as you mention it often in the text

We will include a modified Figure 1 with indications for all mentioned zones: Tidal River, Dollard Reach, Middle Reaches and Outer Reaches.

Figure 2: it is a bit strange that you connect points for nitrous oxide and not for other variables.

We agree with the reviewer that the data presentation in figure 2 is not optimal For the nitrous oxide data, we will modify the plot with plotting 1 min averages along the data to represent our continuous measurements. We will do the same for the continuous FerryBox data. We will keep the other plots as they are, as these represent distinct samples.

About the zones: it took me some time to understand you did not speak about “geographical” zones but more about ..? geochemical? Biogeochemical?

We will clarify that we refer to the biogeochemical zonation of the estuary. This zonation does fit relatively well with geomorphological characteristics of the estuary. Therefore, we chose to name the zones according to the geographical zones. To prevent confusion, we will rename our biogeochemical zones, i.e. “Denitrification zone”, “Coactive zone” and “Outer zone”. However, the results from our two cruises also show that the biogeochemical zones can move along the estuary depending on parameters like river discharge. In 2014, the discharge of the estuary was significantly higher than in 2020 or than the long-term average for August. Together with intense transport of suspended particulate matter downstream, this very likely caused the extension of the denitrification zone further into the Dollard Reach.

L274: zone 1 has not the same extension in 2014 than in 2020. In 2014 the nitrate removal extends to salinity 20, while in 2020 only to salinity 4. Zone 1 has thus not a geographical definition. It is not the “upper riverine part” as mentioned – at least not for 2014… L275: idem for zone 2: in 2014, this zone starts at salinity 20 and extends to the mouth while for 2020 it starts at 5 and extends to 25.

In our text, we refer to biogeochemical zones rather than to geographical zones. We will make this clearer from the beginning in the introduction of the manuscript to prevent confusion. Therefore, we will also rename our biogeochemical zones, i.e. “Denitrification zone”, “Coactive zone” and “Outer zone”. We describe and discuss the shift of spatial extension of the zones in chapter “4.1 Biogeochemical zones in the Ems Estuary” (L284 - 289). The shift of zones may be driven by the increased discharge condition in 2014. Which also affects parameters like salinity and the suspended particulate matter concentration.  

In addition, I’m not sure I can really see the third zone in 2014 from the N data in figure 4. L271: the 3 zones are not clearly appearing from figure 4… L276: I don’t see a third zone in 2014… but there is one in 2020

Zone 3, the outer zone, shows divergent trends in 2014 and 2020. In 2020, figure 4 showed nitrate uptake in the Outer Reaches of the Ems estuary, which we assigned to assimilation caused by a stronger influence of the spring phytoplankton bloom in the North Sea. In 2014, the identification of the outer zone is more difficult, as the outermost samples follow the conservative mixing line in figure 4. However, these outermost samples are distinct from the prevailing processes in zone 2, because they do not show signs of nitrate production / nitrification, a characteristic of zone 2.

Therefore, a zone 3 exist in 2014 as well as in 2020, but is mostly determined by mixing, which makes a clear distinction based on figure 4 difficult. Our PCA supports the results the separation of samples into zone 2 and zone 3 as is shown in figure 5. We discuss the processes in zone 3 in chapter “4.4 Mixing and nitrate uptake in the Outer Reaches” in detail. To prevent confusion we will try to elaborate the separation of zone 2 and zone 3 in more detail.

L368-371: I like very much your mapping approach which allows to estimate the amount of NO3 denitrified and produced by nitrification. However, there are quite a lot of assumptions behind this approach. You could go one step further by comparing these number quantitatively to a nitrate mass balance. Does the net decrease or increase in nitrate corresponds to the calculated balance between nitrification and denitrification?

First, we want to thank the reviewer for the comment. A comparison of our mapping approach to a nitrate mass balance would certainly help to strengthen our obtained results. Unfortunately, as we mentioned in a comment above, our data does not allow an adequate mass balance for the tidal Ems estuary. Overall, our mapping approach allows us to estimate the relative importance of both processes in individual sections of the estuary. To evaluate the results a quantitatively comparison with a nitrate mass balance would be helpful, but is not possible with our data.

To test the validity of our mapping approach, we calculated the net removal based on the integrals below the conservative mixing line. This somewhat more conservative approach, which does not include isotope values,  shows that the net mass calculation results of the mapping approach are valid – notably, they are founded on the same data base as the integrals.

The calculation of integrals naturally does not enable us to disentangle the individual contribution of nitrification and denitrification, which is based on isotope effect calculations. We do not see a way to overcome this, and will emphasize in a revised version that the partitioning between these two processes depends on the underlying assumptions for isotope effects.

L394: a small sink (-16 compared to 160 µmol/l ?)

As we will remove statements about the overall role of the estuary, we will remove this statement and only refer to the source and sink functions in the indivual sections of the estuary.

L396: remove “as well” or remove “strong”. You do not have a strong denitrification zone…

We will remove the word “strong” from the sentence.

L486: “Overall, the Ems estuary acted as a nitrate sink in both years.” You do not really show that the Ems acts as a NO3 sink. To do this you should have done a NO3 mass balance for the whole estuary. Hence you show that there is a zone in The Ems where you have a nitrate sink.

We agree with the reviewer. We will remove this statement and refer to the activity in the individual zones (see comments above).

Editing comments

We thank the reviewer for the thorough revision. We will incorporate all suggested editorial changes.

References

Deek, A., Dähnke, J., van Beusekom, J. E. E., Meyer, S., Voss, M., and Emeis, K.-C.: N2 fluxes in sediments of the Elbe Estuary and adjacent coastal zones, Mar. Ecol. Prog. Ser., 493, 9–21, https://doi.org/10.3354/meps10514, 2013.

FGG Ems: Hochwasserriskiomanagmentplan 2015 - 2021 für den deutschen Anteil der Flussgebietseinheit Ems gemäß §75 WHG, Flussgebietsgemeinschaft Ems, 2015.

UBA, G. central environmental authority: Nationaler Teil der internationalen Flussgebietseinheit Ems, https://www.umweltbundesamt.de/sites/default/files/medien/2466/dokumente/steckbrief_ems.pdf.