Major comments

Overall, the manuscript describes well the results from an interesting experiment. BVOC emissions from these boreal ecosystems are significant on both atmospheric chemistry and radiative properties, through secondary organic aerosol formation. Although not thoroughly discussed in the manuscript, BVOC emissions are coupled to chemical ecology and plant-herbivore interactions and the results will be interesting to ecologists and plant physiologists.

The methodology is interesting: it blends one of the newest and most sophisticated instruments in the field (PTR-ToFs-MS eddy covariance) with one of the oldest methods of ecosystem fluxes: the flux gradient approach with thermal desorption tubes. A strength is the comparison of these two methods. One are for improvement: there have been comparisons between gradient fluxes and EC before, specifically for BVOC fluxes. These previous studies should be further cited in the Discussion.

While the overall study and manuscript are sound, there are a number of details that need to be addressed. For example, the units of fluxes change midway through the paper. They need to be consistent. Also, there are some indications that the current manuscript was carved out of a larger work. Some comments below focus on internal inconsistencies.

Minor comments

• Line 41: you mention acetone, but since you are not presenting results on acetone in this paper, the mention seems out of place.
• Line 75: while the context is mostly clear, it’s helpful to insert either plant or tree speciation, since you are also referring to chemical speciation.
• Line 81: insert “chemical species-specific” before emission factors.
• Lines 94-111: there is a lot of great methodological information in this paragraph, but I suggest some reorganization to improve clarity. You start with PTRs, introduce PTR-ToFs, then discuss EC and go back to PTR-ToFs. Perhaps discuss PTRs and then ToFs, and next discuss EC. While many readers know the basics, BVOC papers are also read by ecologists that have more limited knowledge about the methodology.
• Line 121: do you mean PTR-ToF-MS here? Be clear, since you have already made the distinction above.
• Line 141 (Fig 1): it would be an improvement to add the gradient inlet heights on this figure.
• Line 178: give location of company (Ionimed)
• Line 179: give location of company (Ionicon)
• Lines 215-216: give some statistics about the tilt that was calculated.
• Lines 216-217: did the calculated delay time agree with the delayed calculated from the tubing flow and geometry (lines 165-169)? Also, using this method of maximizing the correlation coefficient can introduce a bias if there is actually no flux. But since multiple compounds are being measured, this probably was not a problem.
• Lines 220: were the tubes in some sort of auto-sampler and collected in-situ on the tower? Or was there a sampling line and the tubes were collected at the base of the tower?
• Lines 248-287: are there also co2 measurements at the tower? Could you check your approach by comparing your results to gradients in co2? There are a lot of assumptions in the theory used here, especially around the gamma factor given in Eqn. 3.
• Lines 289-297 (section 2.7): this is great that you are providing a quantitative error analysis. But given the complexity of the theory presented in the previous section, there is the potential for larger methodological errors. Please provide some literature values that give an estimate of systematic errors that are associated with flux-gradient approaches.
• Line: 336: need to give some more information about the fitting procedure. What statistical approach was used?
• Line 369 (Fig. 3): I am having trouble understanding the foot print information. First, the color scheme is given as red and blue in the figure caption but the figure has green and a very little bit of blue. Second, the green contours are clear, but are there separate blue contours? I can barely see the blue and I am not sure what it represents. Finally, I believe these contours are cumulative flux, but the contour lines should be specific described in the figure caption. I cannot evaluate the statement on lines (365-376) that the two contours agree with each other.
• Line 408 (Fig. 5): give the meaning of the shaded regions for panels (f) and (i).
• Line 461 (Fig. 7): why are the flux units ng/m2/s instead of the nmol/m2/s used in the other graphs? If there is no specific reason to use different units in this graph, pick one unit and be consistent.
• Lines 509-526 (Section 3.3.3): This section is tangential to the rest of the paper. It’s great that you have additional data on different chemical species, but you have not prefaced these results in the introduction. Please remove.
• Line 527: section numbering is not consistent.
• Line 544 (Fig. 9): again, units are not consistent with Fig. 2.
• Line 551: “Based on comparison with 2022 precut TD measurements” I don’t understand what this is referring to.
• Lines 552-555: give ratio of TD/Vocus concentrations for each period. Also, why are the June data not presented?
• Lines 572-575: give ratio of TD/Vocus fluxes for each period. Also, why are the June data not presented?
• Lines 587-590: you write there is not a “substantial variation” but you should use statistical language. Because of your limited dataset, there might be ‘substantial variation’ that you do not have the statistical power to detect. You should simply say there is not a statistically significant difference.