The complex problem of diffusion−reaction inside of bundles of nanopores assembled into microspherical particles is investigated theoretically based on the numerical solutions of the physicochemical equations that describe the kinetics and the thermodynamics of the phenomena taking place. These theoretical results enable the delineation of the main factors that control the system reactivity and examination of their thermodynamic and kinetic effects to afford quantitative predictions for the optimization of the particles' dimensional characteristics for a targeted application. The validity and usefulness of the theoretical approach disclosed here are established by the presentation of the complete analysis of the performance of thiol-functionalized microspheres aimed for sequestration of Hg(II) ions from solutions to be remediated. This allows the comparison of the microparticles' performance at two different pH (2 and 4) and the rationalization of the observed changes in terms of the main microscopic parameters that define the system.