Overview

This manuscript (egusphere-2025-5068) presents a valuable dataset on greenhouse gas (GHG) dynamics across 21 sites in a temperate estuary. The study’s primary strength lies in providing concurrent measurements of all three major GHGs across a spatial gradient from the river mouth to the outer archipelago. The spatial coverage, which captures contrasting habitats (sheltered vs. exposed sites), provides a useful map of GHG hotspots and sinks. However, the manuscript has several methodological flaws and some overinterpretation of results. The authors claim that benthic processes drive observed patterns, despite the lack of direct benthic measurements.

The authors have assembled impressive fieldwork and an extensive measurement campaign. Reframing the manuscript to emphasize its strengths (comprehensive spatial coverage, simultaneous GHG measurements) while providing more details for the method section and acknowledging some limitations (no benthic measurements, discrete sampling) will strengthen the work considerably.

Major Concerns

1. The manuscript repeatedly mentions “benthic processes” and “methanogenesis”, but there are no direct benthic measurements. The authors’ attempt to deconvolve contributions using Apparent Oxygen Utilization (AOU; Figure 6) is insufficient because AOU reflects the net result of all processes (pelagic, benthic, and advective) and cannot isolate the benthic contribution. The authors observe deviations in surface water GHG concentrations from expected salinity-driven patterns and infer benthic processes, but are not really convinced.

2. Unclear gas transfer velocity and fluxes calculation. The authors measured CO2 and CH4 fluxes directly using floating accumulation chambers. However, for the final CO2-equivalent budget in Figure 7, they state they “chose to use the estimated fluxes” (line 350-354). The authors adopted a gas transfer velocity (k) wind parameterization, despite having direct measured flux data, water-phase partial pressure and partial pressure data. These three data points are what are needed to derive their own site-specific gas transfer velocity. With these measurements, the authors would have generated a novel, site-specific parameterization, a valuable contribution for gas transfer velocity parameterizations. The authors’ justification that Randers Fjord is most comparable (line 148) is insufficient. Additionally, several paragraphs in the discussion are more closely related to the method section.

3. The authors describe “in situ” measurement using a custom flow-through system (line 104) but then detail a protocol where they stopped at 21 discrete sites, waiting “until equilibrium was reached (up to 45 minutes)”. This equilibration time is quite long for the LI-7810 analyzer, which has a response time of 2 seconds. Please provide more details on the “custom-built flow-through system” and why it is turning a high-resolution instrument into a 21-point discrete sampler.

Specific Comments

Line 8: “Estuaries remain understudied for GHGs” is overstated. Please moderate language to acknowledge the growing body of estuarine GHG research. Recent literature demonstrates substantial research on estuarine GHG emissions, as shown below.

Line 29: “CH4 and N2O contributed differently as a source and a sink”. This phrasing is wrong. Data show CH4 was consistently supersaturated. Only CO2 and N2O acted as both source and sink.

Line 115: Quite a complete setup, but not sure why there is a complete absence of pH measurements, which significantly limits the validation of carbonate chemistry calculations.

Lines 125-130: Were these floating chambers anchored or drifting (following the current)?

Line 134: The choice to use Borges et al. (2004) parameterization instead of deriving site-specific values is unjustified. I suggest comparing the K600 derived from the floating chamber with the K600 by Borges et al. (2004).

Line 160: If the system was stopped for 45 minutes at each station (line 118), why would there be ‘sharp concentration changes’ or ‘data from transition periods between stations’? This statement is really confused about the actual sampling protocol.

Lines 210-2015: The Results section for GHGs is very thin on statistical description. The Kendall correlation analysis is currently in the Discussion, but is a presentation of results. It should be moved to the Results section.

Figure 5: The “seawater endmember” has a salinity of only 6.36. This is very low for a seawater endmember. What is the salinity range in that region?

Lines 249-256 (Mixing Model) and Line 268 (nTA/nDIC): Details about theoretical pCO2 calculations from conservative mixing and alkalinity/DIC normalization procedures belong in Methods, not Discussion.

Some GHG research papers for estuarine systems:

Yeo, J. Z. Q., Rosentreter, J. A., Oakes, J. M., Schulz, K. G., & Eyre, B. D. (2024). High carbon dioxide emissions from Australian estuaries driven by geomorphology and climate. Nature communications, 15(1), 3967.

Zheng, Y., Wu, S., Xiao, S., Yu, K., Fang, X., Xia, L., ... & Zou, J. (2022). Global methane and nitrous oxide emissions from inland waters and estuaries. Global Change Biology, 28(15), 4713-4725.

Nguyen, A. T., Némery, J., Gratiot, N., Dao, T. S., Le, T. T. M., Baduel, C., & Garnier, J. (2022). Does eutrophication enhance greenhouse gas emissions in urbanized tropical estuaries?. Environmental Pollution, 303, 119105.

Borges, A. V., Abril, G., & Bouillon, S. (2018). Carbon dynamics and CO2 and CH4 outgassing in the Mekong Delta. Biogeosciences, 15(4), 1093-1114.

Please see my comments in the attached document.

Kind regards,

Damian L. Arévalo-Martínez

Overview:

The manuscript „Spatial heterogeneity of GHG dynamics across an estuarine ecosystem” presents a nice data set of GHG data and related variables in an estuarine ecosystem in the northern Baltic Sea. The data set presents a spatial distribution within the onset of the of the salinity gradient, however, it represents just the late summer period. Nevertheless, the data set included next to theCO2, Methan and N2O as well. The main findings are that the estuarine system is heterogeneous, sinks and sources were found for CO2 and N2O, but methane were supersaturated in all samples and were emitted to the atmosphere.

The manuscript is well written and relatively easy to follow, even if you are not familiar with the study site. Although it is known that the coastal waters and estuaries are important for the GHG balance, comprehensive data set with all three most important GHG are still rare, and they are needed to understand these quite heterogeneous contributions.

Major comments:

If next to CO2 and Methane also N2O is included to understand the interaction between these three GHGs, it would be good to introduce next to the Carbon cycle also the Nitrogen Cycle and the interaction between them. At some points the mentioning of N2O not good connected.

One important variable to understand N2O production and emissions is next to the oxygen supply the availability of nitrate and the other DIN, as the authors mentioned in the discussion. Can you present also at least nitrate concentrations and include them in the correlation matrix?

Somewhere in the manuscript the authors must explain what the potential sinks for N2O are and present an explanation for the undersaturation of the N2O. Do you assume that N2O is consumed under anaerobic conditions in the sediments? Are the also processes in the water column which consumed N2O.

The aim of the study which is formulated at the end of the introduction seems to be a bit too ambiguous. I would suggest orientating the aims a bit more on the structure of the discussion section.

The explanation of the importance of the sediments for the GHG production, without having direct measurements comes a bit out of the blue and contradicts the hypotheses that the GHGs are mainly just mixed from the river inputs.

Some specific / minor comments:

Abstract: quite too long and can be more focused.

L21: N2O is missing

L 28: Is Methane always a source and N2O a sink?

L64. There is some literature that N2O production and Oxygen depletion correlated, e.g. in the Elbe Estuary

L 88: What are soft-sediment habitats

L100. What was the partial sampling strategy? From fresh to salty? Each Stations just once, how much on one day….

L231: Did you measure DIN (Nitrate, …)

L 306 ff. Here comes the main concrete results of the manuscript that can be one new chapter