Electrodialytic desalination of cheese whey was carried out using a pair of polymer cation exchange (Nafion 117) and inorganic membranes. The ceramic separator was modified with nanocomposite containing hydrated zirconium dioxide and basic bismuth nitrate. This amphoteric filler provides anion exchange ability of the composite membrane. This property is realized when at least one side of the membrane is in contact with an acidic solution. Ion transport through the membranes was shown to be determined by current, whey acidity, and also by composition of the solution in the concentration compartment of the electrochemical cell. It was shown that whey desalination occurred under overlimiting current. Acidification of whey and decrease of the acid content in the concentrate suppress ion transport. The electrodialysis of whey and nanofiltration permeate allowed removal of up to 80% of the mineral components in 5 h and 40 min, respectively. Preliminary ozonation of the permeate increased the rate of desalination.