| 23 Oct 2025
Spatial heterogeneity of GHG dynamics across an estuarine ecosystem
Abstract. Coastal ecosystems are critical components of the global carbon cycle, exerting a disproportionate influence on the carbon budget despite their limited spatial extent. Estuaries remain understudied despite being dynamic sources of the three most potent greenhouse gases (GHGs): carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Such shallow coastal ecosystems are highly heterogeneous, shaped by strong physical, biogeochemical, and biological gradients. Combined with spatial variability in coastal biodiversity, these gradients strongly shape carbon cycling at both local and global scales. However, large uncertainties persist due to limited and spatially patchy measurements, highlighting the need for improved constraints on GHG budgets and their sensitivity to biodiversity loss and climate change.
We measured surface seawater partial pressure of CO2 (pCO2), CH4, and N2O concentrations, along with seawater physical and biogeochemical properties, and air-sea gas exchange, at 21 sites in southwest Finland (Baltic Sea). Sampling followed a transition from estuarine inner bays to the outer archipelago, covering diverse soft-sediment habitats, from sheltered to exposed areas, across a salinity gradient. Surface water pCO2 and N2O concentration ranged from undersaturated (160 ppm and 9 nmol L-1, respectively) to supersaturated (2521 ppm and 25 nmol L-1, respectively), compared to the atmosphere, resulting in an uptake of -36 and -0.0021 mmol m-2 d-1, and a release up to 220 and 0.0383 mmol m-2 d-1, respectively. CH4 concentrations were consistently supersaturated (19 to 469 nmol L–1) compared to the atmosphere, resulting in a net source to the atmosphere from 0.014 to 1.39 mmol m–2 d–1.
Freshwater input from the Karjaanjoki River and its mixing with seawater mainly determined the overall spatial patterns of GHGs. However, deviations from this salinity-driven control were observed. In sheltered sites within the archipelago, elevated pCO2, CH4, and N2O concentrations likely reflected benthic processes, including enhanced organic matter respiration and methanogenesis in warm, late-summer shallow waters, where limited oxidation favoured CH4 accumulation. At exposed sites, mixing processes had a stronger control, resulting in lower GHG concentrations. Our results show that both physical mixing and benthic processes influence coastal GHG dynamics, with benthic ecosystems playing a key but still poorly constrained role. Air–sea GHG exchanges were dominated by CO2, while CH4 and N2O contributed differently as a source and a sink. The balance between production and consumption processes, particularly within benthic habitats, is therefore critical for understanding coastal contributions to the global carbon budget.
Competing interests: Please see the cover letter.
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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.