Miller and co-workers present an observational study on diel and seasonal cycling of pCO2 and air-sea CO2 flux in a mesohaline reach of the Chesapeake Bay. Based on three years of high-resolution observational data, the authors calculated a set of indicators including gas transfer velocity, gas solubility and air-sea CO2 fluxes. This study paid particular attention on the daily and seasonal cycles of pCO2 and CO2 fluxes, as well as their controlling mechanisms in this mesohaline reach. Their results highlight that pCO2 changes rapidly and across a wide range in a 24-hour cycle, and pCO2 and CO2 fluxes are primarily regulated by temperature effects on biological activity. In my opinion, this is a very well-written paper with useful information regarding the carbonate chemistry dynamics of Rhode River, a shallow mesohaline reach of the Chesapeake Bay. Given the quality of the manuscript, it should be published with a minor revision.

I only have some minor comments, outlined as follows.

Line 93-98: This paragraph outlines your findings and conclusions. It would be best placed in the results section.

Line 101: study location – Although the authors emphasized that Muddy Creek contributes little freshwater to the study area, I guess it would be better to provide brief information regarding the riverine inputs, such as the saturation condition of pCO2, pH etc.

Line 323: better to pinpoint the average surface water temperature in June-November and Dec-May.

Line 358: it’s hard to tell the difference between day and night pCO2 in Fig. 3. Maybe average the day/night pCO2 in a month scale?

Line 457: the effective size of seasonal and day/night k600 is comparable according to Table 2.

Line 626: Fig. 7 - very interesting to see CO2 sources in the daytime, but sinks in the nighttime, which seems contrary to the fact that photosynthesis assimilates DIC in daytime and respiration release DIC in the nighttime. Any comments?

The authors emphasized that the pCO2 and CO2 flux were mainly regulated by temperature effects on biological activity, not the solubility associated with the temperature. I think the authors better to elaborate more about the biological effects. For example, why the study area is more autotrophic during cold months? With higher algae growth? Why it is more heterotrophic in warm months? With higher oxidation of organic matters?

Summary:

In this manuscript, the authors used a non-dispersive infrared sensor to measure high-frequency atmospheric and dissolved partial pressure of CO₂ (pCO₂) and to calculate air-sea CO₂ fluxes in the Rhode River Estuary, a sub-estuary of the Chesapeake Bay. They conducted three years of measurements and analyzed the diel, seasonal, and interannual variability. The continuous data showed a strong seasonal cycle in pCO₂ primarily driven by biological activities. The diel cycle is particularly strong in the summer months, sometimes resulting in the reversal of air-sea CO₂ flux direction within a single 24-hour period. The authors also demonstrated the value of high-frequency sampling of CO₂ system variables. This manuscript presents some interesting carbonate chemistry findings in a sub-estuary of the Chesapeake Bay. However, some clarifications, additional analyses, and a few changes in the figures are recommended before publication. Although the comments below are lengthy, addressing them fully would result in a valuable contribution to the journal.

General comments:

1. The authors might consider the following suggestions to help readers access important information more directly through additional figures in the supplementary material. It’s up to the authors whether they want to include these suggested figures, but as a reader, I would appreciate them, and they could help support some of the statements in the manuscript (such as detailed comments #6 and #8).
   1. Isolate and identify dominant signals using power spectral density. For example, expected frequencies include the solar cycle at 1 day^-1, M2 tide at 1.93 day^-1, S2 tide at 2 day^-1, and possibly the spring-neap tidal cycle.
   2. Would it be possible to plot the diel cycle in pCO2_water as a function of the hour of the day? How does this cycle correlate with the diel cycles in temperature, solar radiation, and oxygen? While I believe that time series of raw data over the years are available in the supplementary material, it is challenging to discern the correlation between these daily cycles from the multi-year time series.
2. Table 2 shows that the season is more important in explaining the observed variance than day/night or their interaction (e.g., Line 416, 483). However, the manuscript emphasizes the large diel cycling associated with CO2 production and consumption (e.g., Figs 2 and 3; Line 391, 464). I found these results somewhat contradictory, mainly due to the large seasonality in the diel cycle. For example, in terms of pCO2_water, the diel cycle is almost the same as the seasonal cycle in the summer (e.g., June, July), but it is much smaller than the seasonal cycle in the winter. Because of the large seasonality in the diel cycle, I’m not entirely sure if it is appropriate to compare effect sizes as in Table 2. Please correct me if I misunderstand anything.
3. I believe a system can still be net autotrophic even if there is a positive flux of CO2 to the atmosphere. External inputs, such as riverine freshwater entering the estuary, can be particularly important. If freshwater entering the estuary via rivers has a high DIC to alkalinity ratio, then it is possible that the estuary is a net source of CO2 to the atmosphere but still be net autotrophic at the same time. In the case of the Rhode River Estuary, external impacts from rivers may not be as large, and CO2 outgassing could indeed correspond with heterotrophic conditions. However, I do recommend being cautious when directly linking CO2 flux and trophic state, especially given that data are presented at one single station.

Detailed comments:

1. Line 50: It is not clear what is meant by 'total inputs.' Is this referring to CO2? If so, it should specify the input of CO2 from the atmosphere to the ocean, as the ocean is an overall sink of atmospheric CO2. Please correct me if I have misunderstood.
2. Line 93: This paragraph appears to be a summary. Personally, I don’t think it is necessary here, as the authors have already included such information in the abstract.
3. Line 112-113: Please convert the area from hectares (ha) to square kilometers (km²) to match other SI units in the text.
4. Line 114: Could the authors please clarify what the largest tidal constituents are at the study site? I wonder if any of the temporal variability in air-sea CO2 flux is correlated with spring-neap tide cycles.
5. Line 254: I'm curious about the purpose of the discrete total alkalinity measurements. Were they used for evaluating sensor pCO2 or for calibration?
6. Line 342: The seasonal variability is clear from Fig. 2. However, for diel variability, it might be helpful to conduct a simple spectrum analysis and directly show the signal. Adding a figure in the supplementary material would be beneficial. Just something to consider.
7. Line 345-346: The label on the y-axis suggests that Fig. 3 shows daytime pCO2_water and nighttime pCO2_water. However, the statement at line 345 seems to indicate that the black and yellow lines represent the pCO2_water range. This is a bit confusing. Please consider clarifying the label on Fig. 3 or the statement in the main text. Additionally, could the authors explain why the oscillations from day to night and from night to day are both included in Figure 3, especially given that they are quite similar?
8. Line 348: It seems that none of the figures and tables show that the morning pCO2_water in the water is the highest. Could the authors plot the diel cycle as a function of the hour of the day?
9. Line 351: Figure S1 doesn’t clearly demonstrate the inverse relationship between the daily cycles of oxygen and pCO2_water. This figure only shows the time series of raw data. Could the authors provide more context? Or did the authors focus on the seasonal variability in oxygen and pCO2_water here? Please correct me if I have missed anything.
10. Line 385: Could the authors provide a range for the 6-hour variability? Here it says 'considerable,' but it is not clear how large the local perturbations are. Table 3 shows the variability in pCO2_air between day and night; perhaps it can be cited here.
11. Line 435: The use of '75%' could be misleading, as it might suggest that biological activities account for 75% of the variability. However, since seasonal variations in temperature and biological activity have opposite effects on pCO2_water, it may not be appropriate to list a percentage here. For example, if the ratio of temperature effect to biological effect (T/B) is 0.99, it does not mean that biological activity accounts for only 1% of the variability; rather, it means that the two effects are nearly equal and cancel each other out. Please correct me if I have misunderstood anything.
12. Line 540: This section is titled 'Diel cycling,' but the diel cycle has already been discussed in previous sections (3.1-3.6). Therefore, it may not be necessary to have a section specifically for diel cycling, especially since only one paragraph is included here. Please consider incorporating this information into other sections for a clearer structure for readers.
13. Line 612: DIC was used previously in the manuscript. Please define it when it was first used.
14. Line 618: Could the authors elaborate on why the interannual variability was attributed to variations in water temperature? It seems that the impact of salinity is also discussed in section 3.6.