The effect of the migration of charged units on the structure of hydrophobically modified polyelectrolyte gels swollen by D2O was studied by small-angle neutron scattering on an example of gels of terpolymers of acrylic acid, n-dodecylacrylate, and 2- acrylamido- 2 -me thyl-1-propane sulfonic acid (quenched charged units) and gels of copolymers of partially neutralized acrylic acid and n-dodecylacrylate (annealed charged units). The content of charged units did. not exceed 20 mol %, so that the electrostatic repulsion was too weak to disrupt the hydrophobic domains formed by self-assembled n-dodecyl chains, which was evidenced by NMR data. It was shown that upon increasing the charge content both types of gels undergo microphase separation with the formation of hydrophobic clusters consisting of several densely packed hydrophobic domains and hydrophilic regions swollen by water, where most of the charged repeat units and counterions are located. The dimensions of the nanostructure of the gels with quenched and annealed charged groups were compared. It was shown that the size of clusters in the gels with annealed charged units is much bigger than that in the gels with the same fraction of quenched charged units. This effect was attributed to a much weaker electrostatic repulsion in the corona of the hydrophobic clusters in the gels with annealed charged groups, because the charged units repelling each other are able to move farther apart.