The manuscript “Multi-scale phytoplankton dynamics in a coastal system of the Eastern English Channel: the Boulogne-sur-Mer coastal area” presents a nice dataset with very high frequency sampling of phytoplankton abundances which is novel and interesting. Below are some general comments while more detailed comments are included in the file enclosed.

Overall, the article is well written, but sometimes it is hard to follow as the authors switch from the results of one year to another. Like for example presenting raw data of phytoplankton abundances for year 2021 and then jumping to a cross-covariance analysis for year 2022. Then my suggestion to the authors will be to focus first on the results from 2021 and then move on to 2022. Presenting the same set of results and analysis for both years so readers can see both and compare them directly.

For the analysis I suggest the authors to include other statistical analysis to see what is driving the abundances of different phytoplankton groups like for example a multivariate analysis like a redundancy analysis that will show how different environmental variables affect different phytoplankton groups. That way readers will see directly which phytoplankton groups behave similarly and what variables are driving the observed phytoplankton dynamics. Similarly, to assess changes in the composition of the phytoplankton community just analyzing the Shannon index is not enough since the index does not inform in changes in composition just changes in relative abundance distribution. To assess changes in community composition the authors may use ordination analysis like nMDS or a linear discriminant analysis, which are classical analysis to study changes in the composition of microbial communities.

In the methods section some important details are missing (see details in the enclosed file) so please include them. Especially the authors need to include a section regarding extreme events since there is established body of literature on this topic and right now it is impossible to say if the authors followed it. For example, they defined a marine heatwave (MHW) showing 90^th percentile of the data gathered during one sampling period and to define MHW 30 years of data previous to the analyzed period are needed to generate proper climatology and then establish the 90^th percentile as a threshold for MHW. Similar analysis should be used to establish extreme events regarding other variables. If these methodologies were not used (or cannot be used due to a lack of data) the authors cannot use the term extreme events or MHW since they clearly defined in the literature. Therefore, they should use a different term to refer these events like maybe “case studies”.

Across the manuscript the authors used Julian Day (they start in January 1, 4713 BC) when they are referring to ordinal day (between 001 and 365), please adjust this across the manuscript.

It is unclear to me how the authors know which species dominated each phytoplankton group determined by the CytoSub since no phytoplankton samples were collected in parallel to calibrate the composition of each group by optical or genetic taxonomic analysis. This is not a trivial detail since across the manuscript the composition of the groups is considered as a given. Therefore, more details are needed regarding how the authors are sure on this and how it can be tested since for example some phytoplankton groups like diatoms and dinoflagellates are very difficult to distinguish based on their pigments as they have the a very similar mixture of pigments. In fact, I think no dinoflagellate is mentioned in the manuscript. Are there no dinoflagellates in the eastern English Channel? That would be strange feature (e.g. Widdicombe et al., 2010) and something that should be discussed in some detail.

The readability of the results section may improve if all the environmental data (including nutrients that now are only shown inf the discussion section) are presented first as time series plots and then phytoplankton abundances, biomass and diversity are presented. It may be a good idea to include also a figure like figure 10 in the article for each sampling year. That way readers can easily see changes in total abundance and community composition before the analysis are shown.

In the discussion a paragraph is missing on how the data from the CytoSub compare to other methods as well as the limitation of this method. For example, the size range of the CytoSub leaves out the larger diatoms and dinoflagellates that may biased the results obtained towards shorter time scales as smaller phytoplankton cells react in shorter time scales compare to larger cells. Similarly, some more context on how the dominant species for each group were established and how reliable these assignments of dominant species are for this area of the English Channel. These limitations are key to understand the reliability of the findings presented.

In the manuscript the authors show how the LSP results changed drastically (almost opposite) in a few days within the same sampling period (see figure 8) so the readers may wonder how representative are the findings presented in the manuscript if the results can change so drastically in a few days. The authors should address this issue and state clearly how it affects their findings and conclusions.

Finally, something the authors should expand in the discussion/conclusion section is the fact that both deployments were shorter than one year so seasonality was not recorded in their dataset which probably biased the results towards shorter time scales. Besides, since the second deployment lasted double (6 months) than the first one (3 months) this feature should also be considered when comparing the results from each deployment.

References

Widdicombe, C. E., Eloire, D., Harbour, D., Harris, R. P., & Somerfield, P. J. (2010). Long-term phytoplankton community dynamics in the Western English Channel. Journal of plankton research, 32(5), 643-655.

This study uses automated flow cytometer data to study the phytoplankton dynamics in a coastal system of the Eastern English Channel during spring in two consecutive years and summer in one year. The authors  are able to retrieve from these high temporally resolved data  information on the abundance and red fluorescence of 11 phytoplankton functional groups (PFGs). These data are used to investigate these groups’ succession and their relation to four extreme events (heat wave, desalination, storms). The study reads very well, the methodology is mostly well described and the findings are nicely illustrated and discussed. Overall, I have just a few comments and suggestions for improving the manuscript. I think after applying these revisions the manuscript is ready for acceptance in Ocean Science.

List of points to consider in revision:

1) The study uses many abbreviations which are always introduced and explained, still it could be helpful for reader to be able to look these easily up in a list of abbreviations.

2)  Although all the relevant protocols for the analysis of the flowcytometer data to PFG abundance and PFG red fluorescence are referenced it would be helpful to briefly summarize the steps how the PFG abundance data and red fluorescence data are converted into relative values (as presented in Figure 4).

3) Table 1: I suggest to add the size ranges of each group to the table.

4) Lines 164-165 should be moved to the discussion.

5) Fig.3-5 add the months under the Julian days for better understanding.

6) Line 179 the 2^nd bracket needs to be revised.

7) Line 180: change sentence to “In addition, the PicoORG group contributed on average with 7 % between March 23rd and March 27 (Jd = 82 and 86) to the total abundance.”

8) Comparison of Fig.3 and Fig.4: please comment also on the correspondence of the groups’ abundances to red fluorescence. Explain further the relationship not only to phytoplankton composition but also physiological state?

9) Line 213: I think it should read “Unfortunately, PFG data …” not wind data”?

10) Figure 6 caption: change “residue” to “residual” and add here 10^4 so it reads: “the the y-axis represents the abundance values (in 10^4 cells mL-1).”!

11) Figure 7 caption: change to “… The black dashed lines represent the estimated linear regression.”

12) Lines 260-263: this text concerns what is presented in Figure 8b (reference is missing!).

13) Line 269: it is unclear to which event (to which figure) this sentence links to – maybe this should be moved to the discussion?

14) Figure 11a) shows for many nutrients the time series data, but only PO43- is discussed – why?

15) Line 309-311: can you add the reference to a figure at which this event is visible.

16) Line 368: I suggest to change “picoorganisms” to “picophytoplankton”.