In the light of the referee comments and your response to the discussion, I would like to invite the authors to prepare a revised manuscript. The comments by reviewer 1 concerning the lack of research questions (echoed by reviewer 2) and the need to better structure of the manuscript should be taken at heart. Reviewer 1 made valuable suggestions to overcome these issues. A long description of the model is acceptable but acceptance for publication in Biogeosciences will require that the model is also used to enhance our insights in the biogeochemical processes being modeled and that these insights are discussed. If the authors insist that the objective of this manuscript is strictly to describe a new model development, its parametrisation, validation and sensitivity, the authors are advised to withdraw the manuscript and submit to GMDD (which has an independent editorial board).

The comment about equifinality (reviewer 2) is an important comment and should be discussed in a separate paragraph. In my opinion the response by the authors is partly off-topic. The referee does not question the need or usefulness of mechanistic models but would like to see a that the authors recognize that given the current data it is difficult to impossible to establish whether all processes included in the model really contribute to the observed fluxes.

The authors did a good job in revising the manuscript in line with the concerns of the reviewers. Nevertheless, the manuscript requires further minor revisions before becoming acceptable for publication:
(1) the comment about equifinality (reviewer 2) echoed by the handling editor in the initial decision was not addressed in the revised manuscript. This is still an outstanding concern. “The comment about equifinality (reviewer 2) is an important comment and should be discussed in a separate paragraph.”

(2) Ask a native English speaker (preferably a colleague in the lab) to check the grammar of the manuscript. The manuscript can be understood but there are several (small) problems with for example the use of the word “the” and “a”, tenses of verbs, ... Carefully check the manuscript for typos and small mistakes. I found many and listed few below. This kind of problems require the reader to read a sentence more than once before it could be correctly understood which reduces the chances that the reader will use and cite your work.

Examples of edits that would improve the readability of the manuscript:

Start the abstract with a sentence that gives the context of the study. Try not to make the abstract any longer than it currently is.
L110-120 should be moved to the method section (between L123 and L124) or should be deleted.
L157 Mention that the model is then used to answer scientific question. Give the question.
L468 Leech should be replaced by leach
L549. Define qualitative labels such “reasonably” or even better don’t use them at all and leave it to the reader to decide whether they find this is a poor, reasonable or good fit. L549 could be deleted. Check the rest of the manuscript for undefined qualitative labels, for example, L573 “well”.
L551 Replace umol by μmol.
L559 Mention the statistical test that was used to test the significance of this increase. If there was no statistical test use “substantially” instead of “significantly”.
L610 Should the r in Mr be written as a subscript instead of superscript?