Dear Lisanne Braat and co-authors,

Thank you for your revised manuscript which addresses most of the reviewers' comments. Both reviewers are supportive of your work. However, you only partly responded to some of the points raised by the second referee. These points are important as they concern the representation of short waves in your model, their influence and the tidal boundary conditions. I therefore recommend you to submit a third version of your paper, fully taking into account the reviewers’ comments (see review below).

Sincerely yours,

Eric Lajeunesse



Review of referee #2:

The authors made some efforts to improve their manuscript, but also only partly responded or even ignored some of my previous comments. I will therefore reformulate the problems that would need to be addressed before the paper can be definitely accepted:

-The representation of short waves in the model is still not clearly explained in section 2.1. According to the elements provided by the authors, it seems that the only effects that is represented is the enhanced bed shear stress due to orbital wave motions. If this is the case, this should be clearly stated around L.21-28. Then, does Tau_cw of eq. (5) stands for “currents & waves”? How is it computed? Does it apply to the circulation model and the sediment transport model or only the second one?

-Tidal boundary conditions. Unlike along the coastlines of the Netherlands, most coastal zones around the world are exposed to tides propagating mainly shore-normal. Why applying an alongshore phase lag to M2 and not a cross-shore one? Why not prescribing tides along the Western boundary?

-The section 4.3 of the discussion totally misses the effects of short waves. As explained in my previous review, an oceanic basin large-enough to have meso-tidal ranges has usually substantial short waves as well. As explained in nowadays numerous published studies (e.g. Bertin et al., 2009; Nahon et al., 2012; Wargula et al., 2014; etc…), short waves drive a range of processes that promote flood-dominance and tend to counteract the ebb dominance that estuaries and inlets develop due to tidal asymmetry. In the absence of short waves, this is not surprising that the authors model predicts continuous enlargement of the estuary mouth, at least without mud. Although the studies listed above rather concern tidal inlets and small estuaries, the processes explained are generic and apply to large estuaries and therefore should be included in the discussion.

Other along the text minor comments
-P5, L5: why “Dyfi, i.e. Dovey”? Then estuary should start with a capital letter.
-P5, L6: “…boundary conditions to address the main question:…”
-P6, L11: “caused mainly”
-P7, L31: erosion rather than degradation?
-P8, L4-8: -P8, L4-15: according to my understanding of Delft3D, bed level changes originate from the horizontal divergence of bedload transport as computed through the Exner equation and erosion/deposition computed as the bottom boundary condition in the suspension transport model. Does the morfac apply to both? Please clarify.
-P8, L26: “differ by two orders…”
-P10, L16-17: if waves impact the bed shear stress in the circulation model, then the current velocities will be impacted and sand fluxes computed by the EH formula as well. Please better state that the EH formula does not represent sediment stirring by short waves.
-P11, L5-6: as already commented in my previous review, why not using a parallel version of Delft3D, parallel computing is nowadays totally democratized.
-P15, L4: you may think that I’m playing with words but, if the elevation and the velocity signals are out of phase by pi/2, this is well a phase lag. I keep thinking that you mean that this phase lag is constant along the estuary.
-P15, L27: coma after notably as elsewhere in the manuscript starts by an adverb.
-P16, caption figure 4: how do you compute the tidal discharge, you remove the freshwater discharged prescribed at the river boundary?
-P20, L3: “irrelevant” is too strong, I would suggest “of limited impact”.
-P24, L26: I would rather say “the effects of short waves on the hydro-sedimentary dynamics of the estuary is limited to the stirring of sediments”.
-P25, L10: coma after “with this in mind”.
References:
Bertin X., Fortunato, A.B. and Oliveira A., 2009. A modeling-based analysis of processes driving wave-dominated inlets. Continental Shelf Research 29, 819-834.
Nahon, A., Bertin, X., Fortunato, A.B. and Oliveira, A., 2012. Process-based 2DH morphodynamic modeling of tidal inlets: a comparison with empirical classifications and theories. Marine Geology 291–294, 1-11.
-Wargula, A., Raubenheimer, B., Elgar, S., 2014. Wave-driven along-channel subtidal flows in a well-mixed ocean inlet. Journal of Geophysical Research: Oceans, 119 (5), pp. 2987-3001.

Dear Lisanne Braat and co-authors, 
 
Thank you for your revised manuscript. It addresses all the comments raised by the reviewers and I am therefore willing to accept it for publication in Esurf, subject to some technical corrections. 
 
In places the manuscript is difficult to follow with some long sentences, that can be confusing for the reader. Furthermore, the passive voice is over used in the manuscript – it would be good if you could replace some of the ‘Our’s with ‘The findings’ or ‘The results show’ etc.. Some of this will also be picked up by the Copernicus proof readers – so making changes at this stage will speed up the publication process later on.
 
I have listed hereafter a few examples of sentences I found particularly complicated to understand and I recommend that you edit these sections to make the points clearer for the readers.
 
Conveying your science clearly is really important and I feel these changes will increase the quality of an already very good paper.
 
Sincerely yours,
 
Eric Lajeunesse
 
 
 
P2 L31 
« Data from the two estuaries indicate that mud is deposited on the sides of the estuary (Fig. 1a–d) shielded from the strongest tidal flow and larger fractions of mud are also found on bars in general agreement with the estuarine facies description of Dalrymple and Choi (2007). The hypsometric curves (Fig. 1g and h) indicate that most of the mud is deposited on the intertidal area, yet, significant fractions are also found in channels. Additionally larger mud fractions are observed in the single-channel upper estuaries (Fig. 1a, d and f). To summarise, 10 − 20 % of the lower estuary cross-section is typically covered by mud, increasing to higher fractions up to about half the cross-section in the single-channel upper estuary. »   
 
 
 
Bottom of page 13: 
« It could be argued that the lowering in Fig. 3e indicates that a true equilibrium was not reached and will not be reached because the river continues to import sand and the ebb delta continues to grow in the near-absence of littoral processes, but for our purposes and time scale of interest Fig. 3j and the timeseries of maps indicate that equilibrium planform geometry of channel, bars and mudflats in the estuary was reached after about 500 − 1000 yr. » 
 
 
page 15, L 25: 
Additionally the duration of the ebb flow is longer (Fig. 4g), similar to the current Dovey estuary where 25 the flood phase takes 5 h and the ebb phase 7 h near Aberdyfi (Brown and Davies, 2009), which is similar to the green line in Fig. 4b. 
 
 
Bottom of Page 15: 
« Since the  duration and the velocity amplitude asymmetry are ebb dominant, cross-sectional flow area is larger for the flood flow otherwise there would be an imbalance in tidal prism, because tidal prism is the multiplication of velocity, duration, and cross sectional area. »
 
page 17: 
« In Fig. 9a–d channels move through a cross-section at the mouth through time, though slower for a larger mud supply. » 
 
page 23: 
In case of marine mud supply the estuary decreases in width near the mouth, but is upstream similar in width and bed level to the estuary without cohesive sediment. 
 
Bottom of page 23: 
When the river becomes more important tidal damping occurs under the influence of increased river discharge by friction (Horrevoets et al., 2004), therefore the point of tidal influence is further downstream decreasing the tidal prism and therefore tidal velocity. 
page 25, L 31: 
Mostly we expect effects timewise, but not in the general pattern and trends. 
 
Page 25 
Marine mud supply causes the development of a muddy coast and in this model only influences the mouth of the estuary, which strongly decreases funnelling of the estuary, but is of little influence in combination with waves though these effect might be underestimated due to uncertainties in wave transport and chosen settling velocities.
 
Page 28: 
Our findings generalise these earlier trends, because our estuary is self-formed, while several bathymetries tested in previous research are strongly simplified or arbitrary chosen and might not represent a realistic state of an estuary, meaning that flood- or ebb dominance could be the result of the imposed combination of initial condition and boundary conditions. 

Dear Authors,
Thank you for your work on this paper - that I am delighted to inform you has been accepted for final publication in ESurf subject to the technical corrections above. There are several corrections - but they are straightforward - and I believe will further increase the quality of a really good paper (I liked reading it!).
All the best,
Tom Coulthard