Parasitic reactions, such as production of hydrogen and oxidation by oxygen, can occur under the operating conditions of flow batteries and other electrochemical systems. Such parasitic reactions can undesirably impact operating performance by altering the pH and/or state of charge of one or both electrolyte solutions in a flow battery. Electrochemical balancing cells configured for addressing the effects of parasitic reactions can include: a first chamber containing a first electrode, a second chamber containing a second electrode, a third chamber disposed between the first chamber and the second chamber, an ion-selective membrane forming a first interface between the first chamber and the third chamber, and a bipolar membrane forming a second interface between the second chamber and the third chamber. Such electrochemical balancing cells can be placed in fluid communication with at least one half-cell of a flow battery.