General comments

Good research on contaminant transport in porous media that needs some improvement and further detail. See my specific comments, they will improve the potential new version of the manuscript.

Specific comments

Line 23….“has been the most widely applied framework in the field”. Last words not backed up by references. Add these papers that incorporate discussion on evidence of the Fick’s law in the field:

- Agbotui, P.Y., Firouzbehi, F., Medici G. 2025. Review of effective porosity in sandstone aquifers: insights for representation of contaminant transport. Sustainability 17, no. 14 (2025): 6469.

- Parker, B.L., Cherry, J.A., Wanner, P. 2022. Determining effective diffusion coefficients of chlorohydrocarbons in natural clays: unique results from highly resolved controlled release field experiments. Journal of Contaminant Hydrology 250, 104075.

Line 30. This sentence does not work as it is. Before “purely physical transport” and then you involve geochemistry. Please, revise the structure.

Line 76. You need to disclose the general aim of the research at the end of the introduction.

Line 76. You need to describe the specific objectives of your research by using numbers (e.g., i, ii, and iii) at the end of the introduction.

Line 199. Insert reference to Parkhurst for PHREEQC.

Line 250. This one looks to me a figure, not a table or an equation. Am I correct?

Line 700. More detail on the acknowledgement. Funding bodies are unclear.

Figures and tables

Figure 3. Make the image larger.

Figure 5. Same here, make the figure larger.

Two figures 11. This is not ok.

Figure 9. Make the figure larger also here.

Right now, near-saturated risks sounding like a convenience assumption rather than a controlled approximation. You explore S_r 0.80–1.0, but (as written) saturation appears prescribed rather than evolving, which is a big modeling decision for landfill liners and many barrier systems.  Please add a short model scope paragraph early (end of Introduction or start of Methods) stating explicitly: (1) saturation is constant in time (if that’s the case), (2) when this is reasonable (e.g., quasi-saturated low gas mobility, slow infiltration variability relative to consolidation time, etc.), (3) when it is not (drying fronts, strong unsaturated flow, gas phase transport). Consider adding a brief comparison to Richards/unsaturated THMC literature (even if you don’t implement it).  And be explicit whether near-saturated here means “two-phase but simplified compressibility” vs “single-phase with effective compressibility.”

You have two verification benchmarks, but the paper itself acknowledges no lab/field quantitative validation.  While this isnt a fatal flaw, you do need to strengthen credibility with additional numerical evidence. Consider adding (1) Grid/time-step sensitivity for one representative case (even a coarse/medium/fine study + one plot at the monitoring point). (2)  Splitting / sub-stepping sensitivity: show that results don’t materially change when the chemistry sub-step size changes within a window (or quantify the trade-off). Your own text highlights synchronisation issues, so you should demonstrate control. (3) For benchmark #2, quantify mismatch: e.g., L2 error vs time, and show it decreases with refinement or explain the irreducible discrepancy (boundary formulation differences are mentioned but not demonstrated).

At minimum, include: (1) The PHREEQC database used, the key input blocks (KINETICS/EQUILIBRIUM_PHASES/etc.), and where they are provided (supplement/Git repo). (2) OpenFOAM discretisation choices for transport (schemes, limiters), linear solvers/preconditioners, coupling tolerances, and convergence criteria (you mention a prescribed tolerance but not what it is). (3) Use a public repository plus archived case files. Without this, the ChemWindow contribution especially will be hard to credit.

At minimum, include: (1) The PHREEQC database used, the key input blocks (KINETICS/EQUILIBRIUM_PHASES/etc.), and where they are provided (supplement/Git repo). (2) OpenFOAM discretisation choices for transport (schemes, limiters), linear solvers/preconditioners, coupling tolerances, and convergence criteria (you mention a prescribed tolerance but not what it is). (3) Use a public repository plus archived case files. Without this, the ChemWindow contribution especially will be hard to credit.

I have some concerns about hybrid decisions. (1)  You use element-based ADE transport, with a weighted molecular diffusion coefficient built from prescribed species fractions, while noting that fully coupled PhreeqcRM could update speciation and thereby D_m dynamically, but you don't do that in this study. (2)  You also include a linear adsorption K_d term in the ADE, while stating that more detailed sorption could be handled by PHREEQC reaction terms. Please add a why this choice paragraph: is the goal robustness and speed? If so, say that explicitly and acknowledge the trade-off. Specify whether K_d is used in the case studies and, if yes, whether PHREEQC includes any overlapping sorption reactions.

You model landfill-liner-like consolidation with chemistry. There are some questions with (1) the mechanical model (elastic vs elasto-plastic/creep typical in clays), (2) the lack of reaction-induced porosity/permeability evolution (I know you already acknowledge this which is good, but it reduces interpretability of long-term plume changes), (3)  boundary conditions (drainage, injection as fluxes at multiple points) and whether they represent a realistic exposure. Consider adding  a short justification for the constitutive law used and explicitly call the case studies “demonstration problems” rather than predictive landfill designs. Add one sentence in the Conclusions about what would change when property feedbacks are included (directional expectation is fine, but label it as expectation).

Also some minor comments below:

(1)  In benchmark #2 you say early-time deviations come from transport formulation and boundary representations; please add one sentence indicating which boundary treatment differs (Dirichlet/Neumann/mixed; inlet formulation), and whether refinement improves it.

(2) Consistently distinguish “hydraulic conductivity K” vs “permeability k” (the symbol list emphasises K).

(3) Injection strengths are given as fluxes at J1–J3; ensure it’s always explicit whether that is imposed as boundary flux (mol/(m²·s)) and over what area.

(4) Computational performance section: helpful, but reviewers will ask for scaling beyond 4 MPI ranks and/or mesh size dependence. Even a small strong-scaling plot (1,2,4,8,16) on one case would help.

(5) Consider moving the limitations to earlier in the discussion.