Electro-Fenton (EF) is one of the most effective processes for treating organic pollutants in water. However, its performance is often restricted by mass transport limitations and slow catalytic reactions. While recent reviews have summarized various strategies to enhance the EF process performance, a focused analysis separating the physical magnetohydrodynamic (MHD) effect on mass transport from the quantum spin-chemistry effect on reaction kinetics—one of the most promising enhancement routes—has not yet been established. Here, this gap is addressed by developing a framework including the four key species of the EF systems: the Fe²⁺/Fe³⁺ redox couple, the reactants (H⁺ and O₂), and the electrons supplied. On this basis, the influence of magnetic fields on each species is examined, clearly distinguishing MHD-driven mass transport from spin-chemistry effects on intrinsic kinetics. This distinction helps resolve ongoing mechanistic debates and provides practical guidance for designing advanced magnetically assisted water treatment technologies.