General Comment:

The authors have resumed their former work to provide further insights in the study of Curonian Lagoon dynamics in a climate scenarios perspective. They have leveraged the modelling setup of the previous study and have stated the aims of their latest study in a clear manner inside a streamlined text. The concept of forcing an hydrodynamic model with accurate information, such as the one coming from an hydrological model, constitutes a better practice with respect to provide climatology derived river water inputs, the latter being deprecated if not, as it might be in some cases, detrimental. Yet some technical aspects of the paper can be ameliorated in two points which most drew my attention:

1. the modelling setup is poorly described in detail. The authors refer to their former paper for the model description, that is not sufficient in that case either in my opinion.
2. the calculation of water fluxes is lacking of some details that deserve to be reported. Please see the comments below for detailed suggestions and offers of reflection.

Authors’ response: 

Thank you for your thorough review of our manuscript. We have considered your comments and suggestions for improving the technical aspects of our paper. Below is a summary of the revisions we’ve made based on your specific points:

1. Modeling Setup Description: We have expanded the section detailing our modeling setup. We now provide a more detailed description of the hydrodynamic and hydrologic model configuration, including the specific parameters, boundary conditions used in our study (section 2.2.).
2. Calculation of Water Fluxes: We have revised the section on the modeling set-up including additional details of water flux calculations. This now covers the methodologies employed and the assumptions made (section 2.2.).

We believe these revisions address your raised concerns and enhance the clarity of our study. Thank you again for your valuable feedback, which has been instrumental in improving the quality of our manuscript.

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lines 38:39 "Apart from the atmospheric models, there is also a variety of ocean models  that have to be considered (Madec et al.,2016, Mellor G. L., 2004, Umgiesser et al. 2004)."

This sentence does not look really coherent (a variety is mentioned but 3 models only are referenced).  The authors should re-formulate the sentence and justify the reference to these 3 specific circulation models.

Authors’ response: 

Thank you for pointing out the inconsistency in our statement. We agree that the sentence could be more precise. We have revised the sentence to clarify our intent and to justify the specific references:

Introduction section: Apart from the atmospheric models, there is also a variety of ocean models, for example NEMO (Madec et al., 2016), POM (Mellor, 2004), ROMS (Shchepetkin and  McWilliams, 2005), MITgcm (Marotzke et al., 1999), SHYFEM ( Umgiesser et al. 2004) and others, that have to be considered.

References:

Madec, G., and NEMO System Team: NEMO ocean engine, Sci. Notes Clim. Model. Cent., 27, ISSN 1288-1619, Institut Pierre-Simon Laplace (IPSL), 2004.

Marotzke, J., Giering, R., Zhang, K. Q., Stammer, D., Hill, C.,; Lee, T.: Construction of the adjoint MIT ocean general circulation model and application to Atlantic heat transport sensitivity. Journal of Geophysical Research: Oceans, 104, 29529–29547, 1999. https://doi.org/10.1029/1999JC900236

Mellor, G. L.: Users guide for a three-dimensional primitive equation numerical ocean model, Princeton Univ., Princeton, NJ, 08544–10710, 2004. 

Shchepetkin A.F., McWilliams, J.C.: The regional oceanic modeling system (ROMS): a split-explicit, free-surface, topography-following-coordinate oceanic model. Ocean Modelling,9 (4),  347-404, 2005. https://doi.org/10.1016/j.ocemod.2004.08.002.

Umgiesser, G., Melaku Canu, D., Cucco, A., Solidoro, C.: A finite element model for the Venice Lagoon. Development, up, calibration and https://doi.org/10.1016/j.jmarsys.2004.05.009, 2004.

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lines 72:74 

The sentence doesn't really look like well-constructed. I suggest something like:

"The lagoon covers an area of 1584 km2, with its widest section stretching up to 46 km in the southern part. Conversely, in the northernmost part (Klaipėda Strait), it narrows down to approximately 400 m wide."

Authors’ response: 

Thank you for the remark, we incorporated your suggested sentence reformulation in the updated version of the manuscript (section 2.1 Study area)

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lines 116:118

The text can be enriched with more details about the shyfem configuration, such as the horizontal resolution, the type of boundary conditions (lateral/surface). Considering the climate context, what kind of interpolation of atmospheric field has been applied to force SHYFEM? What kind of bulk formulation has been applied?

Authors’ response: 

We added additional sentences to the text, lines 175-186.

Horizontal resolution is variable due to the finite element nature of the grid. However, it varies from 250 m close to the Klaipeda Strait to up to 2.5 km in the central part of the lagoon and up to 10 km in the Baltic Proper. The atmospheric forcing has been interpolated directly from the regular grid of the regional climate model data to the finite element nodes by bi-linear interpolation. Lateral boundary conditions have been taken from Copernicus data and interpolated onto the finite element grid (water levels, T, S). The COARE3.0 module is used for bulk formulation.---------------

line 186

Can the authors add more details about the methodology to compute the water fluxes across the section? To this end the authors should address these 2 points:

1. In their previous study (Idzelyte,2023) the authors have split the flow exchange computations in "inflow" and "outflow" in order to assess the variation in percentage in the various scenarios/seasons. Considering that in this study the authors address only fluxes timeseries, does this inflow/outflow distinction applies yet? How is the 10-year moving average computed in this case? When computing outflow in a 10-year window, all the inflow values that fall in the window are set to 0? The author should provide some details about the methodology of computing the time-averaged fluxes.
2. The authors should provide further insights on the computation of water fluxes across the section. In particular they should report their method of assessing the velocity on the straight line represented by the 4 cross sections. For what I can notice from the authors' former publication of 2023, the SHYFEM mesh is not regular in the Curonian lagoon, where the triangles have different size on the coast and in the center. This makes the computation of fluxes in a conservative way quite tricky. The correct way to compute water fluxes on a mesh like SHYFEM's, and considering also the location of SHYFEM's velocities, is along a spline that connects the triangle centers to the mid-edge points. Computing fluxes accurately across straight segments like the 4 proposed by the authors is possible but upon the application of a conservative method of interpolation on the velocity field. Have the authors considered this issue and its possible effect on the uncertainty assessment?

Authors’ response: 

1. Yes, the distinction between inflow and outflow categories still applies in this analysis. The 10-year moving average is computed by first calculating the yearly average flux for both inflow and outflow categories separately. These yearly averages are then used to compute the moving average over a 10-year window. For each 10-year window, we calculate the average inflow and outflow flux by considering all yearly-averaged values within that period. The inflow values are not set to zero when computing the outflow, and vice versa. Instead, both inflow and outflow are continuously accounted for over the entire period to ensure accuracy in reflecting the overall water flux dynamics. We have included a detailed explanation of this methodology in the revised manuscript to clarify the process for computing the time-averaged fluxes. The changes (as written below) can be found in the updated manuscript section “2.4.1 Investigation of hydrological and hydrodynamic model results”:

“In this analysis, we maintained the inflow and outflow categories as in our previous study (Idzelytė et al., 2023). We analyzed the data by computing the 10-year moving average using yearly average fluxes, this way ensuring an accurate representation of water flux dynamics throughout the study period.“

Reference:

Idzelytė, R., Čerkasova, N., Mėžinė, J., Dabulevičienė, T., Razinkovas-Baziukas, A., Ertürk, A., and Umgiesser, G.: Coupled hydrological and hydrodynamic modeling application for climate change impact assessment in the Nemunas river watershed–Curonian Lagoon–southeastern Baltic Sea continuum, Ocean Sci., 19(4), 1047–1066, https://doi.org/10.5194/os-19-1047-2023, 2023.

1. To compute the water fluxes across the sides of the elements, first the conservation of mass in the finite volume around a node that is guaranteed by the continuity equation is used. The fluxes over the lines delimiting the finite volume element per element (a split line that connects the triangle centers to the mid-edge points) are made divergence free by subtracting the storage of water inside the node. With these finite volume fluxes the fluxes over the element sides can be computed. In case of the presence of a material boundary the matrix that connects the finite volume fluxes to the fluxes over the element sides is regular and can be solved directly. However, in case of no material boundary the matrix is singular. In this case one of the flux conservation equations is dropped (it is redundant) and is substituted by a condition of non-rotational flow around the node. This procedure ensures a complete mass conservation over the lines defined on the element sides and is correct up to machine precision.

To the manuscript we will add: “To compute the water fluxes across the sides of the elements, first the conservation of mass in the finite volume around a node that is guaranteed by the continuity equation is used. The fluxes over the lines delimiting the finite volume element per element are made divergence free by subtracting the storage of water inside the node. With these finite volume fluxes the fluxes over the element sides are computed.”

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Caption of Fig.3 "Note the adjusted y-axis ranges" 

Authors’ response: 

Thank you for bringing up this oversight. We have made the necessary corrections in this caption.

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Section 3.1.6

As I understand the authors have used an ice model to force the simulations but I cannot find any reference (I suppose is Tedesco et al. 2009, please add it) nor how it's been nested in the modeling framework. It is not clear whether ESIM2 has forced SHYFEM or it has been used as standalone. I think that the modelling framework description paragraph should be more exhaustive.

Authors’ response: 

Yes, the ice thickness data were derived using the ESIM2 model as presented by Tedesco et al., 2009. The ESIM2 model was operated independently as a standalone model. Its output time series were subsequently integrated as surface boundary input data for the hydrodynamic component of our modeling system. We have now included a detailed explanation of this process in the revised manuscript to clarify the modeling framework. You can find the following updated text in section “2.3 Data”:

“The ice thickness data utilized in our study were derived using the ESIM2 model (Tedesco et al., 2009, Idzelytė and Umgiesser, 2021). This model was run independently as a standalone system, and the resulting output time series were integrated into our hydrodynamic modeling framework as surface boundary input data. This approach allowed us to accurately incorporate ice thickness dynamics into our simulations, enhancing the overall reliability of our model during the ice season.”

References:

Tedesco, L., Vichi, M., Haapala, J., and Stipa, T.: An enhanced sea-ice thermodynamic model applied to the Baltic Sea, Boreal Environ. Res., 14, 68–80, 2009.

Idzelytė, R. and Umgiesser, G.: Application of an ice thermodynamic model to a shallow freshwater lagoon, Boreal Environ. Res., 26, 61–77, 2021.

Technical corrections:

In addition, we correct some small typing errors found after additional proofreading. And we revised our manuscript a lot, based on the other reviewer comments.

General notes

We thank the reviewer for the valuable comments and remarks. We answered the reviewers questions and will revise our manuscript. Detail answers are attached as a supplement.