The unprecedented global water scarcity and shortage of fresh water have drawn attention to an abundant yet overlooked water resource: Brackish ground water. Although the common desalination methods are energy intensive for low salinity water streams, Capacitive Deionization (CDI) offers a highly efficient and economical alternative for desalinating brackish water. In CDI, an electrically charged porous material is employed to remove ionic species from aqueous solutions. CDI includes different multi-scale transport phenomena and requires robust theories to accurately model its performance. In this work, we introduce a dynamic two-dimensional model which couples the diffusion and advection in the bulk solution with the diffusion and electrosorption in the porous material. The significance of this model lies in the incorporation of the transport theories with the adsorption/desorption resistances and non-constant chemical attraction forces in the micropores. A lab-scale CDI unit is employed to validate the proposed model at different transport time scales and electrochemical techniques are used to characterize these systems. Efficiency of the studied cases is also evaluated using the proposed inclusive figure-of-merits, where both numerical and experimental data present a trade-off between adsorption and energetic performance of the systems with low and high mass Péclet number. The results obtained here highlight the significant role of the rate limiting resistance for the ionic species transferring from macropores into the micropores in the porous electrode, especially at low initial concentrations.