Summary: The manuscript presents an analysis of a data set from the Baltic Sea reanalysis, focusing on temperature, salinity, ocean heat content and freshwater content. This data set covers the period 1993-2023. The manuscript investigates long-term trends and the connection between these variables. The conclusions of the analysis are not totally surprising. They identify a warming trend and a strong connection between water temperature and ocean heat content and between salinity and freshwater content.

Recommendation: I have concerns about the manuscript's framing, title, and objectives. I do not see problems with the data analysis. My recommendation is that the manuscript requires substantial revisions.

Main points:

1) The title is misleading. I could not identify any ' new conceptual framework framework' nor find a definition for 'state of the Baltic Sea'. The manuscript is perhaps a valuable presentation of the ocean reanalysis, but it does not present any 'framework#' and leaves many concepts in the title and in the introduction undefined. I think this manuscript is indeed a presentation of this data set, which is fine, but it tries to present it as a more substantial advance than it really  is.

If the authors believe the manuscript presents a new conceptual framework, they should explain it clearly in the introduction. I failed to see it.

2) The introduction often presents the manuscript in a too-bright light. For instance, the text states (line 45) that it presents a 'model'. I cannot see any model. Again, the manuscript analyzes the connections between different ocean and atmospheric variables, but it does not contain any model that would allow predictions or that includes any physical mechanisms, equations, etc.

3) I have problems understanding the 'state of the Baltic Sea'. First, it appears that the manuscript deals only with physical variables and leaves geochemical or biological variables out of the analysis. The use of 'state of the Baltic Sea' on this account alone seems exaggerated. But more importantly, what does 'state' mean here? Is it a snapshot of the ocean at a particular time? Does it mean a more value-centered assessment of the situation in the Baltic Sea (good, bad, etc.)? Readers curious about the title may be vastly disappointed when reading the manuscript.

4) I do not see the need for a Random Forest method. The manuscript applies this algorithm to conclude that the driver for the heat content is the temperature at all layers and that the diver for freshwater content is salinity at all layers. Do we need an RF algorithm? Any reader would be stunned if the results would have been different. Ocean heat content can be directly calculated from temperature, and freshwater can be directly calculated from salinity. I do not see the need or the advantage of using a machine-learning algorithm to identify those connections. They are obvious.

5) On the other hand, the research question is unclear. What knowledge gap would the manuscript fill? What is unknown in the variability of the Baltic Sea that this data set may help to clarify? The introduction is silent about this.

Summarizing these previous points, it seems to me that the manicurist tries to push up a correct and useful analysis of the ocean data by using exaggerated terms (which often do not have a clear meaning)

Particular comments:‭

6) line 33‬ ‭exceptional‬ ‭increase‬ ‭in‬ ‭global‬ ‭sea‬ ‭surface‬ ‭temperature‬

Exceptional in which sense? At which time scale? Th Earth's temperatures have been warmer than now in the geological past.

7) ‭Figure 1‬ ‭: Conceptual Scheme of the Baltic Sea State ‬‭parameters.‬

Again, what is the conceptual scheme shown in this figure? This figure shows the obvious links between those physical variables and only physical variables.

‬8) Some methodological aspects are not clearly explained. For instance, I struggled to find the time scales of analysis. I think it is only mentioned in one figure caption or line 171, which alludes to annual means. I kept wondering for a long time if the authors were anal sing daily means, monthly means, seasonal means or annual means

9) Likewise, it is not all clear whether these variables are considered at the grid-cell scale, water column scale or averaged over the Baltic Sea

10) Often, physical units are missing, for instance, when stating trends. Trends must have units of variable per unit of time. It is not clear if the trends refer to changes per year, for instance, or over the whole period

11) ‭"Surface ‬‭net ‬‭solar‬‭ radiation ‬‭has‬‭ a ‬‭weaker ‬‭but ‬‭still‬‭ significant ‬‭positive ‬‭trend‬‭ of‬ 0.058±0.035,‬ ‭and‬ ‭the‬‭ evaporation ‬‭time ‬‭series ‬‭shows‬‭ a‬‭ negative ‬‭trend ‬‭of‬‭-0.041±0.039"

Units missing

Review of the manuscript “A new conceptual framework for assessing the state of the Baltic Sea” by Raudsepp et al.

Summary: The presented study analyses interannual variations of ocean heat content (OHC) and freshwater content (FWC) of the Baltic Sea based on modern data analysis techniques (random forests) and puts these into perspective to other state variables of the ocean and atmospheric forcing. The underlying data consist of reanalysis products, covering the period 1993-2003. The authors highlight that interannual basin mean FWC variations refer mainly to FWC variations in the halocline, while OHC variations refer mainly to both, variations in the seasonal thermocline and upper halocline.

In a second step, the study elaborates on the potential impact of atmospheric forcing and some oceanographic factors. The authors suggest that similar analysis techniques might be applicable also to other regions.

Major Comments:

The subject of the study is interesting and I appreciate the use of modern data analysis techniques. Also, the manuscript is well written. Still, I have some points which need in my eyes to be addressed:

(1) My major concern is that I find the fitting procedure for the random forest models not well explained. Generally, I would expect distinct data for the fitting procedure and for testing the fit - to evaluate how well the RF-model generalizes to unseen observations. I am not sure if this has been done. Also, I am not sure how the hyperparameters were chosen and would appreciate some more details (e.g., the number of trees, tree depth, minimum samples for splits).

(2) I must admit that I find it sometimes difficult to keep overview over all the RF-models. I would find it helpful if the many random forests would be described in an extra sub-section in the Methods and/or a table of all RF-models mentioned in the text might be nice (including some respective measures of the goodness of fit).

Specific Comments:

Introduction, Ln.38ff: Winsor et al. (2001) and Rodhe and Winsor (2002) might be interesting to mention here for FWC. For OHC Dutheil et al. (2023) might be interesting.

Ln. 55/56: I would suggest rather to talk about Granger-causality here (https://en.wikipedia.org/wiki/Granger_causality) because statistical relationships cannot identify “real” cause-and-effect relationships.

Line 79ff: It might also be interesting to add that many studies reported a strong warming of the Baltic during the past decades when compared to the global oceans (e.g. Kniebusch et al, 2019).

Line 99ff: I would find it nice to get a bit more background information on FWC and OHC – why it is considered so important and how it’s calculated? (e.g. I guess the reference salinity from Raudsepp et al. 2023 has been updated?).

Methods, Random Forest: Line 109ff: As outlined in the major comments, I find the fitting procedure for the random forest models not well explained. Generally, I would expect distinct data for the fitting procedure and for testing the fit - to evaluate how well the RF-model generalizes to unseen observations. I am not sure if this has been done and how the hyper parameters were chosen.

Methods, Line 136: I think it would help the readers if another subsection was introduced, explaining which data were used to generate the random forests, including the thoughts behind the design-choices (e.g. for using annual means and the selected predictors). Given the very limited amount of data I would try to keep the number of predictors as low as possible. Currently, many design information of the RF-models appear in the Result-Section and I found it  sometimes hard to keep overview.

Line 172ff: As said, I would find it easier to follow if the RF-design information would be moved to a respective sub-section in the Methods.

ine 199: Could you provide some measure on the quality of this reconstruction? –  for the readers to rate it against the fit when using all predictors. Also, I am not sure if this intermediate step is needed (couldn’t deep salinity (or Mohrholz, 2018?) be included directly for FWC based on Fig.3?).

Line 199ff: How do these results and design decisions fit to the foregoing findings that the overall interannual FWC variations are mainly due to changes of FWC in the halocline? (as impacting factors I would thus expect mainly P-E, runoff and inflows form the North Sea?). Ultimately, Fig 3d is a nice result and I think it might help the readability to have it a bit more included in the subsequent argumentation.

Line 212 Which criteria were used to identify MLD and UML? Also, I am not sure how to conclude line 216 from this. Maybe this is because I am not sure what is meant by “of the sea”. Can you help me out?

Line 224: So, these were not assimilated?

Line 232: I would call this inflow instead of influx – but both formulations might be right.

Line 235. You lost me a bit here – maybe it helps to mark the strong inflow events in the time series plot and shorten the explanation so it’s easier to follow?

Discussion & Conclusion, Line 250: I miss some more arguments why OHC and FWC are considered so important that they define the Baltic Sea state (as opposed to common measures such as temperature and salinity).

Line 251: I find “the forcing functions” a bit vague here.

Line 270: replace “correlation” by “relation”? (could be non-linear)

Figures:

Fig.2: I appreciate that the authors aim for as many information as possible in this plot but I am struggling to understand the colored dots in relation to the solid lines.

Fig.4: Could you also describe the symbols in Fig.4 c and d in the caption? Line 244 FWC

References:

Dutheil, C., Meier, H. E. M., Gröger, M., & Börgel, F. (2023). Warming of Baltic Sea water masses since 1850. Climate Dynamics, 61(3), 1311-1331.

Rodhe, J., & Winsor, P. (2002). On the influence of the freshwater supply on the Baltic Sea mean salinity. Tellus A: Dynamic Meteorology and Oceanography, 54(2), 175-186.

Winsor, P., Rodhe, J., & Omstedt, A. (2001). Baltic Sea ocean climate: an analysis of 100 yr of hydrographic data with focus on the freshwater budget. Climate Research, 18(1-2), 5-15.

Kniebusch, M., Meier, H. M., Neumann, T., & Börgel, F. (2019). Temperature variability of the Baltic Sea since 1850 and attribution to atmospheric forcing variables. Journal of Geophysical Research: Oceans, 124(6), 4168-4187.

Mohrholz, V. (2018). Major Baltic inflow statistics–revised. Frontiers in Marine Science, 5, 384.