The freshwater demand increases over the years to attend agriculture, industry, and human consumption demand. Water desalination by capacitive deionization (CDI) would be an interesting strategy to provide freshwater for populations suffering of water scarcity in arid and semi-arid regions in which brackish groundwater is available. CDI is an electrochemical technique based on the removal of ions using carbon electrodes. Besides low-cost, activated carbons (AC) produced from renewable sources are also desired due to sustainability demands. In parallel, appropriate routes for disposal or reuse of crude glycerol from biodiesel plants are also a major current concern (10 kg of biodiesel generates ~1.0 kg of glycerol). So, considering the water-waste nexus concept, in this work we proposed the use of crude glycerol as precursor to obtain a new sustainable activated carbon (PGAC), which was employed as an electrode for CDI desalination of brackish water. The crude glycerol is firstly converted to polyglycerol, which is carbonized and then chemically activated. The best desalination performance using the PGAC electrodes was achieved using membrane CDI configuration, applying 1.6 V, providing a stable salt adsorption capacity (SAC) of 27.1 mg of NaCl removed per g of PGAC over 50 desalination cycles. At this condition, co-ion repulsion is minimized and the charging efficiency (QE ) remained close to 100%. The high values of SAC and QE , along with the low cost of PGAC electrode, led to a very low specific energy consumption (2.6 J per mg of NaCl removed), compared to other values reported in literature, making it a potential candidate for use in CDI desalination. In order to further improve the desalination performance, a new cell architecture was proposed, named percolation flow cell (PFC). The PFC cell combines the fast mass transfer rates of the flow-through cell (FTC) configuration and longer residence time of flow-by cells (FBC), in which the flow velocity and electric current fields are perpendicular. Taking advantage of the beneficial aspects of the FBC and FTC designs, the desalination carried out using the PFC was enhanced by 170 %, providing a remarkable water desalination rate of 1661 mg g-1 day-1 at 1.0 mA cm-2 and single pass operation (7.0 mL min-1). Despite these advantages, the high pressure drop (0.12 bar cm-1) imposes a challenging issue for the effective application of PFE cells.