This manuscript presents a marginal sea basin-scale reconstruction of palaeogeography based on the combination of a big dataset including the eustatic sea levels, the GIA and the Holocene sediment accumulation for the Baltic Basin. A comparison between the modelled results and proxy-data-based reconstruction can improve the GIA model parameters, which is important for the study on Holocene sea-level history. I only have minor comments as below:

1. line 130, please explain why ΔSED should be included in the equation of relative sea level.

2. line 305, constant sediment accumulation rate was assumed in the estimation of sedimentation thickness at each time slice. However, sedimentation rate varies largely because of the changes in relative sea level, sediment supply, etc. particularly in coastal zone. Authors made a discussion in the last section of 5.3 for effect of the sediment dynamics. I feel this is not enough and expect an evaluation of the spatial distribution of areas characterized by changing sedimentation rate.

3. line 401, "whereas the Vistula Spit curves shows continuous sea-level fall" should be "whereas the Vistula Spit curves show continuous sea-level rise".

General comments to the submitted manuscript: ‘Paleogeographic numerical modelling of marginal seas for the Holocene – an exemplary study of the Baltic Sea’ by Miluch et al.

The paper describes the paleogeographic distribution of the Baltic Sea during the Holocene. They base their observations on different data sets gathered from different countries along the Baltic Sea. For the reconstruction, they mainly use three parameters: vertical changes of the water level, vertical changes of the landmasses (tectonics and isostasy), and the thickness of the sediment deposits.

The novelty is that they include the latter one. The paper is well structured, and the Figures are certainly relevant for the message.

After reading the manuscript I have some general discussion points left:

1. The spatial resolution of the grid size in the Baltic is not always clear. I have no idea how accurate and variable for instance the input data of the isostacy is, nor of those of the sediment thickness data. In qualitative sense, they indicate for instance at the data in the northern Baltic Sea is sparse, but I have no idea how sparse (in a quantitative sense, how many data points per km²).
2. The spatial interpolation and extrapolation techniques are not always explicitly mentioned. A Table for all parameters including it’s resolution and spatial interpolation technique would be nice.
3. The discussion about the different phases is much based on the glacial history of the area. While reading the paper, I wondered how large the influx from major rivers in central Europe was, and how this differed during the Holocene. These rivers will certainly transport sediments towards the southern shores of the Baltic.
4. The interpretation around the Danish straits is based on very view data and probably also modeled in a very course sense. The authors discuss their results with those over earlier studies and conclude that not all studies for instance have two straits. How comparable are these studies if both studies are based on not a lot of observations, nor have a detailed modeling grid.
5. The novelty is concentrated on the inclusion of sediment thickness data for the Baltic Sea. In the manuscript, the authors talk about ‘sediment dynamics’, ‘sediment budget’, ‘sediment mass’, and ‘sediment thickness’. The paper becomes much more precise when a clear terminology is chosen.

Really like your terms 'thickness' or 'mass'. Perhaps even better 'thickness' and 'vertical changes in thickness'.

'Budget' is perhaps more than you present (with a budget, you normally also mention lateral fluxes in the system).

'Dynamics' is closely related to sediment transport resulting in areas with erosion or deposition and you are not showing that.

More specific comments are included in the pdf-file of the manuscript.