Can you justify the use of such different values for horizontal eddy viscosity and eddy diffusivity? As far as i Know the turbulent Prandtl number, defined as the ratio between eddy viscosity and eddy diffusivity should be close to 1.

In both figure S1 and S2 there are no red or blue lines. adding these colors as written in the text would let the plots more readable

The Oregon State Tidal Prediction model should provide also the barotropic velocity components due to tides. Why didn't you use also these variables as boundary conditions?

This sentence should be revised. Neglecting waves lead to significant errors in which variables? all or only some of them? This work clearly shows that waves can influence the hydrodynamic in some areas of the bay, especially in the outer basin and near inlet 2, but I think that a conclusion that neglecting waves can lead to significant errors should be supported by comparison of the model output with some observations (sea level, u ,v , Temp and Salt) that demonstrates the benefits of including waves in the simulation. I suggest to modify the sentence or to add some statistical index quantifying the improvement of the simulation with waves compared with the one without waves. This also is connected to the sentence in the conclusion at line 606

plot f) of the radiation stress gradients is missing

It is straightforward from figures title but the a, b and c references of the figures are missing. As in line 206 the C of Celsius degree is missing in the temperature plot.

What is the reference period of wave and wind data shown here? Is it the same period of the model simulations? Is the percentage shown representing the percentage of time in which those conditions are present considering the entire observation time? I suggest to add these information in the text.

I can't see the dashed blue line in figure 1a

This is the same caption of figure 3. It must be changed with wave height and Direction.

Same issue of figure 3. the letter references in the plot are missing

The correlation can be negative. It ranges from -1 (anti-correlation) to 0 (no correlation) up to 1 (total correlation). I suggest to correct the definitions.

Can you explain me this sentence? Trade winds may explain the E or NE direction of the wind. Looking also at the spreading of the wind in the W-NW directions in figure 1e and at the positioning of the cost, it seems that W-NW wind direction could be attributed to breeze.

Are you talking of bays in general or only Spanish bays? I don't know, maybe most of the Spanish bays have a negligible contribution from freshwater? However there are places where the freshwater contribution in lagoon is very common, e.g. many lagoons discharging in the Baltic sea (Curonian lagoon, Vistula lagoon, ...). Can you be more specific?

C in Celsius degree is missing

Do you mean "than"?

I think here you want to refer to fig. 4b1 isn't it?

R squared is the determination coefficient, that is the squared value of the correlation coefficient and is different from the definition given before (line 238-239). What is the actual value of table 1?

The C of Celsius degree is missing

The common definition of RMSE for the term between brackets is Model output minus Observation. This however does not affect the result

The definition of the numerical grid is not totally clear. There are no clear correspondences between figure 1a and the highlighted test. The cell size 20x20 is the one in B or C of figure 1a? and why there is no grid in the creeks in figure 1a? How is defined the grid in the outer domain (A in figure 1a)? Is it the same of B?

I think it is better to use SI units.