Review of the manuscript "Transport dynamics in a complex coastal archipelago" by Miettunen et al.

General comments:

The manuscript is very well structured, of appropriate length, and has nice high-quality figures, in my opinion. Further, the text is very easy to read and contains relatively few grammatical or spelling mistakes. So, from this point of view I'm perfectly happy with the manuscript as it is. However, I do have a couple of specific comments regarding science; see below.

Specific comments:

You state in the Model Description (lines 78-80) that open boundary data are from a CMEMS physical reanalysis; can you elaborate on this? Which variables are prescribed at the boundary, and at what time resolution?

Later in the manuscript you state (lines 273-274) that daily averages are used at the open boundary. Surely, SSH data must be available on hourly resolution? How about currents? I'm a little bit concerned that the barotropic transports are affected by the use of daily averages instead of e.g. hourly data. To address this issue, I propose you validate sealevels against tide gauge data inside the computational domain, preferably one station in the south and one in the north, and perhaps validate the differences between these two (model vs. observations in both cases). If the lack of hourly data at the boundary affects the performance of the model close to the boundaries, the modelled transports may still be okay in the inner domain due to the filtering effect of the archipelago, and you may be able to show this in case you have at least one tide gauge in the inner part of the domain (e.g. Turku?). This may be enough if there are no suitable tide gauges near the northern and southern boundaries. If this is not possible, there will be some lingering doubts about the validity of the model setup with the boundary conditions being used (daily averages), and in extension, the conclusions.

As an alternative, would it be possible to rerun the model for a short time period using hourly resolution of the open boundary conditions, and compare with daily averages?

Technical corrections:

Caption for Figure 7: Please add the info that these are northward volume transports (as I think they are).

Line 184: It seems to me that the mean transport in the lower layer in the central transect is close to zero..? (green curve, middle panel)

Lines 253 (and other places): Change "Baltic Proper" -> "Baltic proper" (lower-case "p"). Throughout most of the manuscript you spell with lower-case "p", which is grammatically correct I think (though some authors use capital "P"). However, it is important to be consistent.

Line 313: Please check if this reference should perhaps be "Westerlund et al. (2021), as on github?