The manuscript by Nesbitt et al. presents a comprehensive dataset of various physico-chemical and biogeochemical variables measured in the Gulf and estuary of St Lawrence between 2003 and 2023. There is good transparency and documentation on the data sources and procedures for quality control and I feel this is overall a solid effort to consolidate this dataset and make it readily available with good documentation to the scientific community. I have only some minor suggestions and questions that the authors can consider.

-Use of colors in Figures, in particular Fig 1-2-3 : these figures are not very accessible to readers with color-vision deficiencies. Modifying the symbols used or working with more clearly distinguishable symbol fills offer an easy fix. See suggestions in Figure preparation guidelines offered on the EGU journals’ website.

-L91 mentions that much of the presented have been exploited in previous publications, but Table 1 does not provide citations for many of the cruises where data were collected – does that mean e.g. that data from cruise 1-13 have not been published previously ? This is not quite clear.

-L184: total nitrogen: is this really total (particulate + dissolved) nitrogen, or should this be total dissolved nitrogen (sum of inorganic DIN species and DON) ? The methods information in the supplement does not make me any wiser, since it just mentions it was measured on a TOC analyser but not whether or not samples were filtered and if so, on what type of filters

-it might be useful to mention for each of the parameters which fraction of the data were flagged as questionnable, and whether there are any patterns in this (e.g. from certain cruises, certain cruise days, etc.)

-L327: “indicating the presence of unidentified alkalinity”: yes, or: a problem with the pH data or issues with carbonate system equilibrium constants used ? The discussion on carbonate system inconsistencies is an important one, and also points out the difficulty in applying a systematic quality control procedure as done for the other parameters.

-several of the plots show a couple of data that visually really jump out, and for which it’s not clear to me why they were not flagged. For example:

Figure 8, DSi versus nitrate for the upper SLE has one datapoint well above the rest of the data.

Figure 9, AOU vs nitrite for Sfjord: one sample point deviates from all others.

Figures 12-13-16: 2 datapoints somewhat above and below 100m depth at Saguenay Fjord jump out with markedly higher salinity, TA, and d18O-H2O. That is internally consistent, but still very odd. Could this point to mislabeling or evaporation during sample storage ?

Figure 13 pHTS at Gulf of StLaurence: one exceptionally low pH seems highly unlikely.

-Figure 11 and corresponding text: provide regression info for water isotope relationships (rather than mentioning the slope is close to 8)

Nesbitt et al. describe a quality-controlled compilation of biogeochemical observations in the Gulf and Estuary of St. Lawrence for the period 2003-2023, using in-situ measurements from different cruises. This dataset is valuable as data compilations of biogeochemical parameters in estuaries and coastal regions are still rare.

However, the structure of the manuscript needs to be revised, as there are numerous repetitions and the sections could be better organized. Moreover, the manuscript and metadata of the dataset lack a thorough description of the uncertainties on the measurement and calculation of the carbonate system variables and especially of the pH measurements in a context of high salinity range.

 Major comments:

1. In section 3, Data collection, please add the total number of data points in the description of the product. This section also lacks a more detailed description of the distribution of the data in depth in the water column (L. 168-170). Are there stations/regions with only surface samples or have all stations been sampled at different depths?
2. Consider adding a column for in-situ pH calculated from pH_TS_measured and for depth to the dataset.
3. Please be consistent with the abbreviation for pH and choose one, as several are used in the manuscript and supplementary material (pH, pH_TS, pH_T) and it can be confusing.
4. Consider adding a description of the results of the primary QC (number of flag=3, for which parameters etc).
5. In section 4.4, I understand that the authors want to use the same constants as used in GLODAP and CODAP-NA for consistency. However, these two data product don’t have data in rivers or estuaries, and the data compilation presented here is based on data from a region strongly influenced by low-salinity waters. Therefore, as described in lines 284-289, the use of other constants, more suitable for low-salinity or cold waters, would have been more appropriate and would have allowed for a more in-depth discussion of the carbonate system parameters.
6. All the subsections of section 4.4 should be moved to another section. In these subsections, results of the qualitative QC are described, therefore they belong in a “Results and Discussion” section and not in “Methods”. Also, please consider changing the data product code of the calculated carbonate variables the to facilitate the use of the product (replace space by underscore and remove the brackets).
7. In general, in section 4.4.1 to 4.4.4, further quantification of the uncertainties related to the measurement methods, choice of constants and organic alkalinity contribution is needed to fully understand the errors and limitations associated with the calculation of pH and other carbonate system variables from pH. In light of all these uncertainties, I wonder whether it is possible to discuss the internal consistency of the carbonate system parameters based on this method.
8. L. 301-302: Here you find that the calculated pH is underestimated compared to the measured values. Can you elaborate on this result regarding the influence of the use of Lueker et al (2000) constants for the calculation and the mention on lines 188-189 that these constants lead to a possible overestimation of pH (the opposite of what is found here).
9. L. 305-309: Elaborate on the methodological source of uncertainty. Which samples or cruises are affected? Please quantify the uncertainty related to the measurement methods and add it here or in the supplementary when the uncertainty and precision of each method is developed. And are these data flagged as questionable if the measurement uncertainty is high?
10. L. 309-313: Please quantify the uncertainties related to the choice in the carbonic acid dissociation constants and the possible impact of organic alkalinity on the calculation.
11. L. 331-334: Move this paragraph at the beginning or the end of this section 4.4.2 as it is currently in the middle of two paragraphs describing regional specifications and as it affects both paragraphs. Moreover, please quantify the uncertainty in the calculation of TA as it is calculated from pH. Same for line 353 with DIC.
12. In section 4.5, Lines 406 to 412 and 418 to 434 describe results and discussion of the QC and not methods. They should be moved to another section. The same is true for sections 4.6 and 4.7 where some paragraphs should stay in method and others should be moved in a “results and discussion” section.
13. The section 5 contains repetitions from previous paragraphs (example: L. 533 to 537 with lines L. 177, 199-200, and L. 208-214). Please rephrase or consider removing the repetition.
14. For Figures 12 to 17, if no description of these figures is made in the paper, they should be removed from the main manuscript.
15. Most of section 6 has already been described in subsections of section 4. To avoid repetition, I suggest to move the paragraphs describing results and discussion that I highlighted earlier in the “method” to this “discussion and validation” section and to review them with the information already in this section 6.
16. The section 6.4 “Data limitations” would benefit from further discussion and quantification of the limitations of the data compilation, measurement methods and QC.

Minor comments:

1. 167: provide instead of provides.
2. 196-197: Repetition of L. 149-150.
3. 202: “Both discrete samples and CTD…” This sentence can be removed as the parameters included in the dataset were already described previously in the last paragraph of section 3.
4. 211-213: Consider adding a map with the location of the three Channel areas in the supplementary material.
5. 233: Where do the regional reference profiles come from? Please add a citation or any relevant information about these profiles.