Cell-cycling performance in capacitive deionization (CDI) can suffer from various charge-efficiency loss mechanisms. In conventional CDI, we show that salt residue within electrodes introduces a temporal lag between charge and desalination stages of a CDI cycle. Without accounting for this effect in the collection of effluent, significant performance degradation occurs as current density increases. To overcome this we use pulse-flow operation to control fresh-and brine-water concentrations. The charge and energy efficiency performance between the two flow-modes is compared using a porous electrode model that is calibrated and validated with experimental data. To quantify specific contributions to charge efficiency losses, the model captures local salt variations resulting from a combination of electrosorption, leakage current, and immobile surface charge. Compared to traditional continuous-flow operation, simulation results show that charge efficiency increases up to 23% in the pulse-flow operation at a current density up to 20 A/m(2), which leads to a 73% decrease of specific energy consumption (SEC). In addition, the SEC predicted by the pulse-flow operation model closely aligns with the predictions of the continuous-flow model after accounting for the temporal lag in effluent salinity. Both simulations and experimental results suggest that pulse-flow operation closely approximates the performance in continuous-flow operation. (c) The Author(s) 2017. Published by ECS. All rights reserved.