Humanes et al. examined intrapopulation variation in bleaching within an Acropora population over a relatively long-term thermal stress. While it’s long been an observation that individuals vary in bleaching intensity and mortality during a natural bleaching event, the authors are correct that this variation has not been well quantified, particularly within a population harboring relatively homogenous Symbiodiniaceae communities. It seems that the physiological indices used herein are well suited for predicting bleaching outcomes based on DHW, and agreed with recent reports of bleaching within the population. Overall, I found this study to be well developed, interesting, and timely. However, there are some issues in the description of the study methods and design that MUST be clarified before publication. Pending that these can be clarified in revision I would recommend the paper to be published.

Methods clarification needed:
The replication in this study was very hard to follow.
Line 188-189: Here it says “all 5 replicates”
Line 368: said 6 fragments per coral,
Line 373: “six experimental tanks, one fragment per colony”
When I went back again, I saw that one fragment went to a control tank but the fate of these was never mentioned again.
But, say there were 102 colonies X 5 fragments each (not including controls) = 510 fragments, but in Line 122: heat stress response was observed in “most of the fragments (96%, n=544). I can’t make this math work even if adding back in the controls?

Minor comments
Introduction
Line 88-89. Please better define degree heating weeks in the text and include explicitly how it’s calculated within the methods. Outside of coral scientists it can be confusing as to how corals experienced 9+ DHW within a 30 day experiment.

Line 94: Persistence of tropical coral reefs is definitely uncertain but I don’t think the persistence of corals in general is. Some species will make it through.

Line 110-115: In these “methods at the end” formats, it’s important to contextualize the results a bit more than usual. The authors could add more context among the individual results or within this last paragraph of the introduction. It would be helpful to have a quick rundown of the temperature profile. There is an implication that “week to months” long heatwaves were studied in this “long-term: experiment. It is relatively long-term but it was not months here. I don’t think including “the heat stress conditions used during the experiment” in the results is enough.

Line 127: is this “6-days bleached” before they died? I was assuming so until I saw fig. 1 with some variation in color changes.

Methods:
Line 361: Just curious why the hottest month shifts around so much.

Line 456-459: was the chl and symbiont density done only as a methodological test against the RGB values? Why not look at those numbers directly? Though I can see why quantifying with just a photo is less destructive. In line 283 the authors say that it was one of the metrics used but I don’t see where it really comes into use as a direct metric in the study.

Discussion: I think the discussion is well written and makes some great points, particularly about how this information can be used in restoration.

The authors have done a good job of addressing the reviews.