The escalating global water–energy nexus crisis necessitates the urgent development of resource-efficient desalination technologies that bypass the carbon-intensive footprints of traditional thermal and membrane-based processes. Current electrochemical deionization frameworks, such as Capacitive Deionization (CDI) and Battery Electrode Deionization (BDI), are often hindered by the high synthesis costs and environmental liabilities associated with synthetic, petroleum-derived electrode materials, which frequently exhibit suboptimal ion-transport kinetics under varying operational regimes. To address these critical bottlenecks, this research explores the pyrolytic transformation of Arenga pinnata (Kaong) nutshells—an abundant agricultural byproduct—into a high-performance, bio-based porous carbon cathodes for integration into advanced BDI architectures. The study focuses on leveraging the inherent lignocellulosic microstructure of the Kaong precursor to synthesize a hierarchically porous membrane capable of efficient NaCl sequestration. The experimental methodology involved the systematic evaluation of the synthesized cathode’s performance metrics, specifically focusing on ion removal efficiency, effluent stream concentration profiles, and Salt Absorption Capacity (SAC). A multi-parametric analysis was conducted to examine the influence of hydrodynamic and thermodynamic variables, namely volumetric flow rates and system temperatures, on the electrosorption phenomena. Statistical validation was rigorously performed using Analysis of Variance (ANOVA) and Tukey’s Honestly Significant Difference (HSD) tests to ensure the reproducibility and significance of the observed data. The results reveal a significant inverse relationship between operational temperature, flow velocity, and SAC; specifically, lower thermal environments were found to significantly enhance electrode wettability and ion-trapping stability. The optimal performance threshold was identified at a temperature of 15 °C and a flow rate of 5 mL/min, conditions which facilitated maximum desalination efficiency through improved interfacial contact and reduced ionic mobility resistance. Ultimately, the findings highlight the viability of Arenga pinnata-derived bio-carbons as sustainable, cost-effective alternatives to conventional electrodes, promoting a circular economy model within the water–energy sector. This study provides a foundational blueprint for future innovations in long-term electrode stability and the application of bio-electrochemical systems in treating diverse feed water sources, contributing to the advancement of sustainable materials in the global transition toward smart energy management.