Van Dam et al used three independent approaches, including Ra-224 decay balance, core incubation, and porewater profile fitting, to calculate/estimate benthic alkalinity fluxes in the sediment of both the southern North Sea and the western Baltic Sea. Part of the data used in this study have been published elsewhere. The authors also explored porewater stable carbon isotopes as well as the relationships between various parameters (alkalinity, DIC, excess SO₄^2-) for possible reaction mechanisms, for example, likely carbon source to porewater DIC, processes responsible for DIC/alkalinity changes. The overall conclusion is that benthic alkalinity fluxes in the studied regions are substantially smaller compared to the results obtained from prior studies in these areas, even though the estimates do vary because of the different approaches taken in this work.

The manuscript is largely well written, and the authors have done a good job tying together both historical and more recent collected data and applying the three techniques to examine fluxes. The detailed geochemical analyses, for example the interpretation of porewater stable isotopes and apparent reaction stoichiometry, are very informative. That being said, this work on one hand lacks some details on the methodology in the geochemical analysis and modeling, for example not all reported porewater constituents have corresponding analytical methods (NO₃^-, K⁺ etc) and none of the methods has precision information, and the parameterization of the PROFILE model seems to offer no context regarding where these values are from; it also seems to bog down in details of flux values of many constituents coming from different methods while there is little quantitative understanding of indeed how much benthic alkalinity is exported to the water column on a regional scale, other than the fact that the values are much smaller than thought. It may be of interest to readers to show the flux ratios of constitutes that could be illuminating for understanding overall reaction stoichiometry (e.g., carbonate dissolution/precipitation) based on the PROFILE model calculations, and perhaps complement the discussion with both the stable isotopes and porewater ratio information, so the latter two do not necessarily stand alone. In the end, the authors stated that seasonality of this flux needs to be researched, among other things. However, given the fact that data from the four cruises already spanned different seasons, it is unclear why seasonality cannot be addressed here, or at least some effort can be taken in this work.

The PCA analysis is interesting, although it also provides little quantitative knowledge on understanding benthic fluxes other than showing that both study region and sediment particle size matter for benthic fluxes, which is not surprising but hardly unexpected. The choice of the input parameters also seems arbitrary and more contextual information is needed if the authors decided to keep this section.

In figure presentations, the authors almost exclusively used bar charts, and some of the figures (Fig. 4) uses fairly complex notation schemes. It will serve readers better if the authors could consider using correlation plots as an additional visual aid to compare and contrast values of the same nature but obtained from different means.

Below are some detailed comments:

Fig. 1 add coordinates axes to the map.

L112, spell out IOW even though it appears in the affiliations already?

L113, is it HCl too?

L133, “at IOW” appears twice.

Section 2.2, please list the precision for all constituents analyzed, even if they may have appeared elsewhere for example prior publications. Later in the text, for example Fig. 4, it seems that not all solutes are mentioned in this section.

Section 2.4—2.6 seem to be more appropriate as subsections of 2.3 (2.3.1, 2.3.2, and 2.3.3) because 2.3 lays out all three techniques but sections 2.4-2.6 elaborate them.

L179, only DIC and Ra were measured? In fact, sections 2.4-2.6 lack general information on what were collected and modelled. Even though the lab analysis section (2.2) mentioned analytical methods for porewater parameters, it is unclear whether all or parts of the parameters were used for all incubations/modeling studies. For Table 1, are these values part of the input? If so, how were the values obtained?

Fig. 2, there is no discussions on Ra-223 throughout the text, where does this information come from? In figure caption please note these sites are from the North Sea.

L236, if TA values are reported to the second decimal place, it would imply that the precision only reached 0.1 mM or 100 µM at best as by analytical chemistry convention the last digit is used as an estimate, then the bottom-pore water TA difference of 2-4 µM appears unrealistic, please clarify.

L237, briefly state the method that Voynova et al. (2019) used to inform readers.

L240-241, in Table 2, TA flux at the maximum 33.6 µmol/m2/hr, but the statement that two prior studies reported results “more in line” values is confusing. Please clarify as these values are nowhere close to what’s reported in this section.

“237.5-275” should be either 237.5-275.0 or 238-275. Significant figures matter.

L248-249 and L254, are they the same thing? If so, merge to reduce redundancy.

L291, the larger NH4+ flux may have organic matter breakdown component as well, see L300. If DNRA is an important process, some references to back it up would be helpful.

Fig. 5, it seems that the site label and data points are misaligned so it’s difficult to see where some data points are from.

L343-344 is repeated in. L350.

L350 paragraph, Site 1 is said to have methane as the possible organic carbon source, here the authors suggested that shallow O2 penetration and high MSR together with sulfur recycling does not lead to net sulfate reduction. As this is a “mud” site, the interpretation seems counterintuitive as marine sediments of this nature in general would see a reduction in sulfate concentration (high MSR rate and low permeability).  

The authors measured alkalinity fluxes and other related geochemical parameters in North Sea and Baltic Sea sediments.  A key strength of the study was the use of a wide variety of approaches to estimate alkalinity fluxes.  The work is interesting and topical given the possible role of alkalinity production in mediating CO2 uptake in the coastal ocean.  Overall, although the text was generally well written, this work felt like a rough draft rather than a polished manuscript ready for submission.  The tables and figures were generally poor quality in terms of their visual appeal and ease of interpretation.  The methods were incompletely described and the results and discussion unfocused. 

Specific comments

Ship board incubations – I don’t understand why fluxes of DO, TA and DIC (and nutrients) were not measured in these incubations?  This is probably one of the most common approaches (along with chambers) for measuring fluxes.

Methods what was the precision of the TA analysis and all other methods?

I don’t think the fluxes presented for Fe, Mn, Ca, H2S, K and HSO4 (SO42-) were meaningful as these solutes either oxidise (H2) and precipitate (Fe, Mn), or the small concentration differences between the sediment and the water column are probably random (especially without information on precision). 

Figure 2 and others.  Label the x axis!

Figures 3 and 4 are a bit overwhelming and hard to interpret.  Can the authors find a way to present the data more clearly (this will be easier when the analytes noted above are dropped).

Results and Discussion

I would suggest that results and discussion be separated.  This will allow a more focused discussion on the key points of interest.  At the moment there is a lot of focus on details and jumping across different ideas.  What are the key factors controlling alkalinity production based on your data set?  It might be helpful to separate muds and sands into different sections.

I don’t think the PCA plot helped us understand the geochemistry here.  This approach is useful when the a-priori mechanistic links between variables is unclear.  I think the links between the geochemical variables here are well known and understood and the interpretation of the PCA plots just re-iterates this understanding.

The miller-tans plots suggest carbonate dissolution is important, particularly in the North Sea sands.  It is noted this contradicts low porewater Ca concentrations, but I doubt if the method has sufficient precision to really make this assessment.  Also, it is likely dissolution and precipitation are occurring simultaneously?

Conclusion

Pyrite burial is suddenly mentioned as a factor in alkalinity production with no prior mention in results or discussion.