Dear editor, dear authors,

I reviewed the paper in detail, and the tutorial cursorily. The case for the model introduced by the authors is made convincingly, and the model clearly falls within the scope of GMD.

Although the model consists of existing components that have been augmented and linked, there is enough new material in the paper to justify publication in GMD. The relevance for practical applications is explained well by the authors. 

The tutorial could use a few more references (including links) to established methods/techniques/software that the authors used. Examples of established software used  are Notepad++ and QGIS, which are given without link or reference. Several links to other useful resources are given in the text of the tutorial, but not included in the reference list, which is a bit inconvenient.

The tutorial explains the working principle of PEST very well, which was quite helpful. But the Morris method used for the global sensitivity analysis used by PEST++ appears without explanation or reference.

All in all, I have no major comments. A few unclarities and inconsistencies appear in the text, highlighted in the minor comments directly inserted into the text. I suspect the inconsistencies are textual, rather than substantial, and can therefore be removed by a suitable rewriting of the text. I do not think the model code itself needs corrections. If this assessment proves to be correct, minor revisions should be sufficient.

Sincerely,

Gerrit de Rooij

This paper presents a new coupling of two existing models, SWAT+ (watershed hydrology) and MODFLOW-NWT (groundwater flow). The coupled model is more hydrologically complete than either of the models on their own, and would be a useful tool for many regional hydrological studies. The paper falls within the scope of GMD, and I believe that it will be fit for publication after minor revisions have been completed. I think that this paper and the tool it describes are useful, but certain explanations need to be clarified and figures in particular need some work to aid the reader’s understanding.

This paper provides an updated coupling after a 2020 paper (referenced Bailey et al., 2020a in the paper) already linked SWAT+ and MODFLOW. The motivation given for the new paper is that SWAT+ has been modified extensively over the past 5 years. One question that I have is whether the new linkage will be able to absorb future improvements to SWAT+, or will brand new couplings be required every few years as modifications continue?

The paper links to a tutorial document, executable file, and sample input data to attempt reconstructions of the simulations presented. I appreciate this effort and the inclusion of the sample data. However, as a Linux user, I was unable to run the .exe file. Source code is provided; it would be extremely helpful to include compilation instructions.

Line 90: The paragraph starting at this line seems repetitive and unnecessary. Can it be integrated into the above paragraph?

Figure 1: This This figure needs some work, e.g. both the Arkansas River and the San Joaquin River have the same symbology, so maybe it would work better to use the same symbol and then just specify on which panel does it refer to which river. What are the small black dots on panel B? Why does panel C have the additional aquifer information while panel A does not?

Line 163 states that for the JMR, the aquifer boundary is the same as the watershed boundary (Fig 1B), but Fig 1B does not actually show this – it would be clearer if explicitly shown or mentioned in the caption.

Are aquifer boundaries shown in this figure and mentioned in the text from an external dataset? Table 2 includes aquifer thickness but it is not clear if this dataset also defines the boundaries.

Line 173 begins a description of population grid cell properties for the MSJ-LC model. Why are these needed for only this model, and not for JMR? Conversely, why is JMR MODFLOW data included in Table 2, but not MSJ-LC MODFLOW data?

Line 181: What is meant by a ‘geographic connection’? Was the data reprojected using GIS?

Line 187: How were the averages weighted? Based on layer thickness, or something else?

Figure 2: Why are we seeing geologic units for one aquifer, but hydraulic conductivity for the other? I'm wondering if the intention is to show two different types of setup/ simulation depending on your aims, but if so, that has not been made clear in the text.

Figure 3: This figure is very blurry.

Line 233-235 and Figure 4: I am confused by the differentiation between options A and B. A makes sense since water will percolate downwards from the unsaturated soil profile; in B, why is exchange only possible from aquifer to soil profile? This implies that the water table can only rise in this case?

Lines 252-261 and Figure 5: On what scale are the HRUs constructed? Are they vectors? Is each agricultural field its own HRU? What else defines an HRU?

Additionally, I thought that the cell size was 500 m (from line 162), but the quoted HRU sizes in this paragraph don’t match with that.

Figure 8: This figure has helpful information, but I feel like I, as the reader, am having to do too much work. Having a reference for what all of these abbreviations mean closer to the image e.g. in the caption would help a lot.

Lines 403-406: What is PEST++? Is it different from PEST? While references are provided, a very brief explanation would be helpful.

Figure 10: What is recharge in all of the areas that are left white?

Figure 12: Is this the change from the model or from the well data? How do the two compare to one another?