Water desalination using capacitive deionization (CDI) has been a recent topic of intense research as a novel technique for water desalination, capable of returning a fraction of the input energy during the regeneration of nanoporous electrodes used for ion adsorption. Usually, a set of consecutive and alternating desalination-regeneration processes is conducted to evaluate the performance of this type of systems under different operational conditions (applied electric potential, flow rate, and initial solution concentration). However, the effect of timing for desalination and regeneration processes on the performance of a capacitive deionization system has not been explored yet. This paper analyzes the effect of varying the duration of desalination and regeneration processes on overall system performance for three different salinity levels and three different CDI system sizes. More specifically, the variation in energy recovery ratio, thermodynamic efficiency, and net energy required per moles of salt adsorbed per unit of volume treated are evaluated. To optimize the timing for transient operation, one desalination test was performed until total saturation, which is identified by the outlet concentration returning to inlet concentration. From this experiment, three characteristic times were obtained: one that minimizes the outlet solution concentration, one that gives the highest adsorbed ions per energy input and one that corresponds to maximum average adsorption rate. The results obtained from testing these three timing strategies in an alternating desalination-regeneration process suggest the existence of different optimal operational points, depending on the specific needs, such as maximum desalination rate or maximum energy efficiency. The methodology presented in this paper can be extended to other operational conditions/systems to optimize their energetic performance. © 2013 Elsevier B.V.