Electrochemical behavior of the electroactive polymeric hydrogels based on polyaniline (PANI) and polypyrrole (PPy) was studied by applying 50,000 galvanostatic charge–discharge cycles. Influence of repetitive electrochemical charge–discharge on the structure of hydrogels was followed by SEM, WAXD and FTIR techniques. The PPy-based hydrogel was found to be more stable demonstrating capacitance retention of 73% and 45% after 5000 and 50,000 charge–discharge cycles, respectively. The decrease in electrochemical performance of PPy can be attributed mainly to overoxidation of the conducting polymer, associated with the formation of hydroxyl and carbonyl groups connected to the pyrrole rings. In the case of PANI, crosslinking of the conducting polymer during electrochemical cycling can be proposed. This leads to micro-syneresis inside the hydrogel and to the formation of porous structure at the initial stages of cycling. During long-term experiment, the crosslinking leads to the formation of a covering layer on the surface of a hydrogel and to masking of its porous structure and decreasing of degree of PANI crystallinity.