Dear authors,

the two Referees have reviewed the revised version of your manuscript and found significant improvements. However, according to their assessment (see the individual referee reports in the manuscript overview) there are still important shortcomings that need further improvement.
In addition, I have identified some issues as listed in the following comments.

1) I consider the micrometeorological interpretation as insufficient and partly problematic. The objective of the study (as stated in the introduction) was to identify the isotopic composition of vertical layers in the boundary layer and to test the capability of the system to provide reliable vertical profiles of the isotopic composition.
The authors should consider that a vertical profile in the micrometeorological sense is always a time-averaged profile over typical averaging intervals of about 30 min. In this way, the turbulent fluctuations (temporally and spatially) can be integrated. Alternatively to a temporal average, a spatial average (on constant heights) may yield the same result, but only if the surface is sufficiently homogeneous.
Therefore, the authors should consider and discuss, whether the instantaneous point sampling is sufficient and useful for micrometeorological profile analysis. It should be discussed whether a longer sampling time (e.g. using a capillary at the inlet, e.g. with repeated valve openings) would be more useful and possible with the sampling platform.

2) The issue addressed in comment 1 also has implications for the interpretation of the differences between the two parallel samples. I do not think that this instantaneous and small-scaled differences represent "systematic features". If they are not due to sampling/analysis problems, they represent local turbulent fluctuations. But two instantaneous samples are probably not enough to provide insight into the turbulence dynamics.
Please consider this in the formulation of the second objective in Section 1 and in the discussion in Section 4.

3) page 8, line 15/16: Indicate the (horizontal) position of the UAV profile measurements in Fig. 4 and/or Fig. 11

4) The newly introduced Fig. 3 is quite interesting but I have the following suggestions for improvement:
a) I am not sure if the indicated sequence in the figure caption "hover, climb, descent" corresponds to the A, B, C sequence of the figure panels. Please give precise attribution in the Figure caption.
b) It would be useful to indicate the position of the sample inlets relative to the propeller blades and the simulated induced flow fields.
c) Indicate the (simulated) ascent and descent speed in the Figure caption.

5) According to Figs. 5 and 6, the wind direction during all flights was between 0 and 90 deg corresponding to north-easterly wind directions. This would mean that the Eddy Covariance tower measured flux footprints outside of the polder area shown in Figs. 4 and 11 (and distant from the water sampling). Please comment on that.

6) Add length scales to Figs. 4 and 11. This is important to relate the horizontal extension of the polder to the profile measurement heights.

Please consider the above comments and the referee comments (see separate reports) in your further revision.

Best regards
Christof Ammann

Dear authors,

You made some improvements in the recent revised version. However, I am not satisfied with some author responses and revisions. I still consider some micrometeorological interpretation as insufficient and problematic. The text modifications partly went into the wrong direction. This necessitates some considerable improvements of the manuscript text as detailed below.
The following comments mainly refer to the editor and referee comments of the previous review (with some additional comments at the end). The page and line numbers refer to the newest revised manuscript version.

EDITOR COMMENTS 1&2 (of previous review)

a) With one (or a few) dozen of grab air samples, it is not possible to determine small-scale variabilities in the boundary layer in a meaningful and quantitative way. As mentioned in the abstract (page 1, line 20), the parallel samples should mainly be considered as a mean to check the reliability and reproducibility of the profile measurements (see also Comment of Referee#1 below). Thus, I recommend to remove the 2nd objective (page 4, lines 3-4) and the corresponding statements elsewhere in the text.

b) page 3, line 1-6: Remove this newly introduced paragraph. It is erroneous or misleading. You totally misinterpreted my original comment. The typical 30 min interval is generally used in micrometeorology to measure and calculate quantities of the boundary layer and turbulence (not just means but also variations, covariances, fluxes, spectra, etc.). This interval comprises most occurring eddy sizes and therefore prevents undersampling.

c) It still needs to be discussed whether the instantaneous point sampling is sufficient and useful for micrometeorological profile analysis.

d) page 3, line 4-6 (and page 12, line 8): This is an erroneous/misleading interpretation of the results of Schaller et al. (2019). They clearly concluded that the episodic 'outburst' events are not connected to soil emissions but to atmospheric dynamics (non-stationary or intermittent turbulent mixing).

REFEREE#1 COMMENTS (of previous review)

e) I do not accept the response of the authors about the "different perceptions of the mixing process". From a micrometeorological perspective, mixing never amplifies concentration gradients or differences but always acts to reduce them. Thus, I want to enforce the critics of Referee#1 concerning the statements on page 12, lines 15-17. These statements should be rephrased or omitted.

REFEREE#2 COMMENTS (of previous review)

f) I want to enforce Comment 2 of Referee#2 that the second objective (page 4, line 3-4) is unclear. The statement "...which require the development of new methods for understanding turbulent mixing processes" is not formulated as an objective. Considering my comment a) above, the second objective should be removed.

ADDITIONAL COMMENTS

g) page 4, line 2: Remove or rephrase the new last part of this objective ("...and therefore the spatial origin ..."). The identification of the spatial origin of the samples/layers is not provided in this study.

h) page 4, line 10: Change "constant" to "near constant"

i) Fig. 3 caption: Rephrase to "Simulation of the relative vertical flow velocity (Vrel) induced
by ..."

j) page 6, line 15: I guess this should read "3913 min^-1"

k) page 11, line 24: Correct to "...except for the last ..."

l) page 11, line 30: Clarify to "...that are not mixed across the inversion."

m) page 13, line 1: What is the specific meaning/purpose of "instantaneous profiles"? Did you mean "simultaneous profiles" here?

n) page 13, lines 5-6: Better write: "to determine vertical differences ..."

Please duly consider these comments in your further (hopefully final) revision.

Best regards
Christof Ammann

Dear authors,

you performed the specifically requested modifications in the text. But it should be clear that other closely related parts of the text also need to be adjusted (in particular concerning my previous comments (a) and (e). Especially Section 4.2 still contains misleading and confusing statements as well as repetitions. The response to my previous comment (c) was not at all satisfying. Therefore, more improvements are necessary before publication.
It is not possible to give detailed suggestions for modifications in every case. However, I try to be as specific as possible in the following list of comments.

Christof Ammann
AMT Associate Editor


SPECIFIC COMMENTS

1) page 10, line 27/28: I suggest the following modification: "Small-scale differences in methane isotopic composition can be introduced by intermittent vertical mixing processes, which may also be induced by the quadrocopter system itself."

2) page 11, line 1-3: This is a confusing statement. The previous sentence describes the systematic vertical difference (layering) in the delta values. Such a vertical gradient is not primarily due to small-scale inhomogeneity but rather due to a significant local ground source in combination with stable stratification (i.e. a lack of vertical mixing).
I suggest to modify to: "This shows that the observed systematic vertical differences are not caused by measurement uncertainty, but are due to local emissions in combination with limited mixing due to stable stratification."

3) page 11, line 13/14: Rephrase to: "However, that latter value has been determined experimentally for long laboratory time series, while the uncertainty may be lower for subsequent analyses."

4) page 11, line 16: Omit "systematic"

5) page 11, line 18/19: This statement is a repetition of lines 11-15 and thus can be omitted.

6) page 11, line 20/21: The statement in the first sentence is not fully true (only for the first four flights) and, as it applies to only one set of four values, it may be purely random. The second sentence is confusing and not scientifically sound. Thus, I recommend to omit both sentences.

7) page 11, line 22-25: This paragraph should be integrated into the normal text flow.

8) page 11, line 27/28: "...and the differences in delta values show a similar height profile for subsequent flights." I cannot see these 'similar height profiles' in Fig. 9 and 10. Thus, I suggest to delete this part of the sentence (or to be more specific in the explanation).

9) It still needs to be discussed whether the short sampling time of 1.3 s can yield representative information of the methane and isotope concentration (profile).
E.g. in page 11, line 30 it could be added: "However, the very dynamic circulation process around the quadrucopter and the short sampling time of only 1.3 s have to be taken into account."


ADDITIONAL TECHNICAL AND LANGUAGE CORRECTIONS

10) page 2, line 30/31: "... to determine contributions from isotopically different sources to the dominating source". This is a confusing formulation, please rephrase.

11) page 10, line 21/22: Change to "...during stable atmospheric conditions (Wolf
et al., 2017), as these prevent mixing with..."

12) page 13, line 27: For clarification please modify to: "...the associate editor Christof Ammann..."

13) page 14, line 34: Remove Denmead et al. (1998) from the reference list, as it no longer occurs in the text.