The self-rearrangement of polymer networks based on a polyelectrolyte complex (PN-PEC) resulting from electrostatic interactions between chitosan (CHT) and chondroitin sulfate (CS) was studied in different swelling pH and swelling time conditions. Analysis of the swelling degree and WAXS profiles revealed that the PN-PEC dried sample can self-reorganize depending on both the swelling medium pH and the swelling time. The reorganization is supposed to result from the rearrangement of PN-PEC-forming polymer chains after the release of part of the CS chains, mainly at pH values closer to or higher than the pKa of CHT. This reorganization contributes to increase the crystallinity, thermal stability, and average pore size of the polymer network. This phenomenon makes it possible to treat PN-PEC to obtain some interesting application characteristics.