Isomorphous substitution is the process that substitutes one atom for another in the structure of clay minerals at the time clay minerals form. This leads to net negative charge in the mineral. Examples are the substitution of Al3+ for Si4+ in tetrahedra and Mg2+, Fe2+, Fe3+ and others for Al3+ in octahedra within clay minerals. Importance of isomorphous substitution is that it produces a net negative charge in clays. This charge must be balanced by positive charged ions from solution. This is important for retention of plant nutrients (soil fertility) and the retention of charged pollutants.
Thus, isomorphous substitution is a mechanism for the creation of charges on soil minerals.