1. The authors try to convince the reader that harmonic analysis of Chl-a over the Indonesian seas may show spring-neap variability associated with tidal currents and baroclinic tides, which may provide evidence of strong tidal mixing in the region. They also show the semiannual and annual cycles. The logical structure of the presentation and the writing are very good; however, in my opinion, at this current stage, it is not ready for publication at the AGUSphere. They focus more on data gaps and processing and lack physical and dynamic mechanisms that can motivate the reader to understand the relationship between tidal harmonic and chlorophyll-a concentration and tidal mixing. There is only one line (line 125) in Section Results, "the potential relationship …". This should be more elaborate in the Introduction and Discussion sections.

2. Southeast Asia Seas/Indonesian seas are strongly influenced by monsoons which drive seasonal variability of the ocean dynamics and climate, seen in the SST, chlorophyll, rainfall, etc. (see, i.e., Aldrian and Susanto, 2003). They present semiannual and annual chl-a cycles. However, in the paper, no mention of or word on monsoon. Had they collaborated with local scientists may help in the results/interpretation of oceanic and atmospheric conditions of Indonesian seas. During the northwest monsoon (boreal winter; wet season), most regions will be covered by clouds and much more clouds/rainfall during La Nina. Hence, during the northwest monsoon from October to April (6 months), it is hardly seen a reliable daily map of chl-a. Hence, Figure 1 and their results may skew toward the southeast monsoon (dry season). Maybe they may have to divide the data availability based on monsoon seasons. Ray and Susanto (2019) show that atmospheric tides may be due to ocean tide (air-sea interaction) and vary with the monsoon. Susanto and Ray (2022) recently showed that tidal mixing in the Indonesian seas varies with the monsoon, ENSO and IOD.

3. Does their seasonal harmonic analysis show the seasonal chl-a due to tidal frequency at seasonal cycles, monsoon, or both? If both, can we separate them?

4. I am curious about high MSf amplitude in the northern coasts of the Lesser Sunda Island (LSI) and what mechanism generates these features. Is it due to monsoon or other dynamical processes? During the southeast monsoon, upwelling (high chl-a concentration) occurs along the southern coasts of the LSI. Meanwhile, upwelling during the northwest monsoon occurs along the LSI's northern coasts, and downwelling during the southeast monsoon (i.e., Wirasatriya et al., 2021). Similarly, seasonal upwelling occurs in the Malacca Strait (i.e., Mandal et al., 2021).

5. They discuss the amplitude and phase of the Chl-a spring – neap tide. Please add a more physical and dynamic mechanism that relates the tide and the peak of Chl-a.

Minor:

1. Ref. Capuano et al., 2022 cannot be accessed because it is in the submission process. I am not sure about the rule of EGUsphere.
2. Link to the software repository does not work.

Some references below may be relevant to the topic which may be added in the citation:

Susanto, R. Dwi, and Richard D. Ray, Seasonal and interannual variability of tidal mixing signatures in Indonesian seas from high-resolution sea surface temperature, Remote Sensing, 2022, 14, https://doi.org/10.3390/rs14081934

Mandal, Samiran, Susanto, R. Dwi, and Balaji Ramakrishnan, Dynamical Factors Modulating Surface Chlorophyll-a Variability along South Java Coast, Remote Sensing, 2022, 14, 1745. https://doi.org/10.3390/rs14071745.

Mandal, S., N. Behera, P. C. Pandey, A. Gangopadhyay, and R. Dwi Susanto, Evidence of a Chlorophyll “Tongue” in the Malacca Strait from Satellite Observations, J. Marine Research, 2021, 233, November, https://doi.org/10.1016/j.jmarsys.2021.103610

Wirasatriya A., R. Dwi Susanto, Kunarso, A. R. Jalil, F. Ramdani, A. D. Puryajati, 2021. Northwest Monsoon Upwelling Within the Indonesian Seas. International Journal of Remote Sensing, 42:14, 5437-5458, DOI: 10.1080/01431161.2021.1918790 https://www.tandfonline.com/doi/full/10.1080/01431161.2021.1918790

Siswanto Eko, Takanori Horii, Iskhaq Iskandar, Jonson Lumban Gaol, Riza Yuliratno Setiawan, R. Dwi Susanto, Impacts of climate changes on the phytoplankton biomass of the Indonesian Maritime Continent, Journal of Marine Systems, 2020,103451, ISSN 0924-7963, https://doi.org/10.1016/j.jmarsys.2020.103451.

Ray, R. and R. D. Susanto, 2019: A fortnightly atmospheric ‘tide’ at Bali caused by oceanic tidal mixing in Lombok Strait, Geoscience Research Letter, 6:6, https://doi.org/10.1186/s40562-019-0135-1

Aldrian, E. and R. D. Susanto, 2003: Identification of three dominant rainfall regions within Indonesia and their relationship to sea surface temperature, International Journal of Climatology, 23, 12, 1435-1452, doi: 10.1002/joc.950.

The authors performed a harmonic analysis of 20 years of MODIS chl data in the Indonesian Seas and concluded that “in some regions chl is phase locked with the spring-neap cycle, peaking around 6-7 days after the local maximum of tidal currents”.  It is an interesteing topic, but in my assessment the paper needs much more work before it is publishable. 

As the authors clearly state, the time series of chl only has data at most 50% of the time due to cloud coverage, and in many regions it is as low as 7-14%. I am not convinced that this is sufficient temporal coverage to support the finding of a  fortnightly signal. The authors state this it is sufficient but present little actual analysis to back this up. Given this is a region strongly impacted by monsoons (which is not mentioned in the paper) I imagine that there could be quite long periods with no data.  They need to do a better job of assessing the gaps in the data and convincing the reader that it is not problematic to answer the question posed here.   

I was curious why they used the GlobColour MODIS product rather than their merged product. The GlobColour project merges satellite data from different sensors which should result in a product with slightly better spatial coverage. Additionally, there are known issues with recent data from the MODIS sensor, which is 15 years past its design life. Using a merged product like GlobColour or the ESA OC-CCI product would mitigate the impact of the declining data quality of the MODIS data.   

They need to do a better job of introducing the study area and describing what is already known about tidal variability in this area, and what big questions still need to be answered.  They don’t even mention the study area in the abstract except for in the last sentence.  Reading just the abstract one might assume this was a global analysis that happened to highlight dynamics in the Indonesian Seas.  Additionally, the conclusion cited above came from the Conclusion section, the abstract was much more vague on the actual results of the paper. 

There are a lot of details about the data analysis or their results  that are glossed over or are vague:

• Lines 34-35. “We have found that least-squares harmonic analysis is adequate to quantify variability”
  
  How was this assessed?  What is their definition of “adequate”? What would be inadequate?  

• Lines 65-67. They state that the noise of the harmonic constants was compared to the amplitude at “fake” tidal frequencies and found to agree well.
  
  What is meant by the “amplitude estimated at “fake” tidal frequencies”? Compared how?  What is their definition of “agree well”?
• Lines 79-80 “it is evident that the seasonal variation of chl-a is 50% or more of the mean in many coastal areas”. I’m afraid this is not evident to me.  Is this from a comparison of the mapped values in Fig3a and 3b?  The two panels have different color scales which makes comparisons between them more difficult.     
• Lines 114-115 “The harmonic analysis… appears to provide more consistent classification…”
  
  Based on what? What is meant by "consistent classification"? 
• They frequently make comparisons to their results and those of others that require some degree of graphical representation, ie lines 117-119, 128-129, 114-115.  
• Line 121. "The fortnightly Chl maximum lags the spring tide... for the examples cited in the Results Section" 
  
  They need to be more specific about what results (or areas) they are referring to.   
• Lines 157-158.  “in some regions chl is phase locked with the spring-neap cycle, peaking around 6-7 days after the local maximum of tidal currents”. Where is this shown? What figure?  

Figure 1. Convert the values shown to percentages.

Fig 4, 5 and 6.  It would be easier for readers to interpret the maps if the colorbar legends for phase were expressed as months rather than radians.