Flowing electrode capacitive deionization systems (FE-CDI) have recently garnered attention because of their ability to prevent cross contamination and operate in uninterrupted cycles ad infinitum. Typically, FE-CDI electrodes suffer from low conductivity, reducing deionization performance. Utilization of higher mass loadings to combat this leads to poor rheological properties. Herein, Ti3C2Tx MXene was introduced as 1 mg mL−1 slurry electrodes in an FE-CDI system for the removal and recovery of ammonia from simulated agricultural wastewater. The electrode performance was evaluated by operating the FE-CDI system with a feed solution of 500 mg L−1 NH4Cl running in batch mode at a constant voltage of 1.20 and −1.20 V in charging and discharging modes, respectively. Despite the low loading, Ti3C2Tx flowing electrodes showed markedly improved performance, achieving 60% ion removal efficiency in a saturation time of 115 min with an adsorption capacity of 460 mg g−1. To understand the high adsorption performance of the electrodes, physiochemical and structural analysis was done via a variety of characterization techniques such as SEM, TEM, XRD, DLS, and Raman spectroscopy. Cyclic voltammetry and galvanostatic charge/discharge profiles were obtained to evaluate the electrochemical properties of the electrodes. The system proved to be an energy-saving technology by exhibiting a charge efficiency of 58–70% while operating at an energy consumption of 0.45 kWh kg−1. A 92% regeneration efficiency showed that the electrodes were stable and suitable for long term and scalable usage. The results demonstrate that MXenes have the potential to improve the FE-CDI process for energy-efficient removal and recovery of ammonia.