Dear authors,

On the basis of these reviews and my own evaluation, the manuscript requires a minor to mandatory revision.

1. Although the authors have mentioned the verification of the BioRT model in the revised manuscript (The BioRT module had been verified against CrunchTope under different transport and reaction conditions (Figures S1 – S7 in SI)), the performance and verification of the model can be further improved. Especially, this is a Model description paper, so it will be helpful for the readers and users if the authors can provide some statistics in the main text (maybe at the discussion section?) for the performance of BioRT compared to CrunchTope (maybe a summary table from those materials in SI?)

2. Please remove the reference from the abstract (GMD - Submission (geoscientific-model-development.net)).

3. Please provide the doi from zenodo for the data and code section. (https://www.geoscientific-model-development.net/policies/code_and_data_policy.html)

4. The authors have responded to original reviewer #2 that the Nash Sutcliffe efficiency has been removed. However, the revised manuscript L660-661 (The model outputs followed the general trend of stream DOC measurements (NSE = 0.55 for monthly DOC) still has NSE with only the abbreviation.

Would you please address this carefully?

5. L487: “It requires much more data and can be computationally expensive but can be used to identify “hot spots” of biogeochemical reactions within a watershed”

What kind of data? Please be more specific.

Please address the above comments, and let me know if you have any further questions.

Best,
Min-Hui

Dear Authors,

Thanks for submitting the revised manuscript. I have two more issues for you to address in the revised manuscript.

Thanks for further illustrating the meaning of NSE (i.e., NSE rangers between -infinity to 1, with NSE = 1 being the perfect fit (Moriasi et al., 2007)); however, can you move to the 1st time when you introduce NSE index?

Please also provide the doi from zenodo for “Documentation, source code, and examples”, which now is only from the github link: https://github.com/Li-Reactive-Water-Group/BioRT-741 Flux-PIHM.

Please let me know if you have any questions.

Cheers,
Min-Hui