Capacitive deionization (CDI) is a promising electrochemical technology for water desalination that can contribute to reducing water scarcity. At the same time, appropriate routes for the disposal or reuse of liquid wastes are also a major current concern. Based on the water-waste nexus concept, this work demonstrates that crude glycerol from biodiesel plants can be successfully used to obtain a new sustainable activated carbon. After polymerization, the crude glycerol was carbonized and activated to obtain polyglycerol activated carbon (PGAC), which was employed as an electrode for CDI desalination of brackish water. Evaluation was made of the electrode performance and stability over cycles of electrosorption/desorption, using different cell configurations (symmetric, asymmetric, and membrane CDI) and cell voltages (Ecell). It was observed that maintaining the potential of zero charge of the negative and positive electrodes outside their working domains during the cycles enabled minimization of that part of the applied potential deviated to co-ion repulsion, consequently improving the salt adsorption capacity (SAC) and charge efficiency (QE). Furthermore, maintaining the potential of the positive electrode below the oxidation potential by controlling the applied Ecell could ensure electrode stability. The best desalination performance using the PGAC electrode was achieved using the membrane CDI configuration (at 1.6 V), resulting in stable SAC (∼27.1 mg g−1) and QE (∼100%) over 50 cycles. The low cost and high SAC and QE values suggested that the PGAC electrode could be considered a potential candidate for use in CDI desalination.