A method of operating a multi-stage electrochemical treatment system (500, 700, 800, 900) having a first stage (510, 710, 810, 910) with at least one electrochemical treatment device comprising a first cell stack, and a second stage (510, 710, 810, 910) with at least one electrochemical treatment device (550, 750, 850, 950) comprising a second cell stack, the first stage in fluid communication upstream of the second stage and the multi-stage electrochemical treatment system further comprises a polisher device (780, 880, 980) at the end of the treatment process, the method comprising: introducing a liquid to be treated to an inlet (505, 705, 805, 905) of the first stage (510, 710, 810, 910); measuring a total dissolved solids concentration and a flow rate of the liquid to be treated at the inlet of the first stage; calculating a limiting current density for the first stage (510, 710, 810, 910), wherein calculating the limiting current density for the first stage (510, 710, 810, 910) comprises calculating the limiting current density for the first stage (510, 710, 810, 910) based in part on the total dissolved solids concentration of the liquid to be treated and the flow rate of the liquid to be treated; operating in the first stage (510, 710, 810, 910) at a first current density across the first cell stack, the first current density below the limiting current density for the first stage; removing a first amount of total dissolved solids from the liquid, in the first stage (510, 710, 810, 910), to produce a partially-treated liquid; withdrawing the partially-treated liquid from an outlet of the first stage (510, 710, 810, 910); introducing the partially-treated liquid to an inlet of the second stage; measuring a total dissolved solids concentration and a flow rate of the partially treated liquid at the inlet of the second stage (510, 710, 810, 910); calculating a limiting current density for the second stage based in part on a measured total dissolved solids concentration of the partially-treated liquid and a measured flow rate of the partially-treated liquid; operating in the second stage (510, 710, 810, 910) at a second current density across the second cell stack, the second current density below the limiting current density for the second stage (510, 710, 810, 910) and lower than the current density of the first stage (510, 710, 810, 910); removing a second amount of total dissolved solids from the partially-treated liquid, in the second stage (510, 710, 810, 910), the second amount of total dissolved solids being less than the first amount of total dissolved solids to produce a treated liquid; wherein operating in the first stage (510, 710, 810, 910) further comprises operating at a first liquid flow velocity through the first stage (510, 710, 810, 910) and operating in the second stage (510, 710, 810, 910) comprises operating at a second liquid flow velocity through the second stage (510, 710, 810, 910), the second liquid flow velocity being greater than the first liquid flow velocity; providing the treated liquid at an outlet of the second stage (510, 710, 810, 910); and removing by the polisher (780, 880, 980) a last fraction of dissolved solids from the treated liquid. introducing a liquid to be treated to an inlet (505, 705, 805, 905) of the first stage (510, 710, 810, 910); measuring a total dissolved solids concentration and a flow rate of the liquid to be treated at the inlet of the first stage; calculating a limiting current density for the first stage (510, 710, 810, 910), wherein calculating the limiting current density for the first stage (510, 710, 810, 910) comprises calculating the limiting current density for the first stage (510, 710, 810, 910) based in part on the total dissolved solids concentration of the liquid to be treated and the flow rate of the liquid to be treated; operating in the first stage (510, 710, 810, 910) at a first current density across the first cell stack, the first current density below the limiting current density for the first stage; removing a first amount of total dissolved solids from the liquid, in the first stage (510, 710, 810, 910), to produce a partially-treated liquid; withdrawing the partially-treated liquid from an outlet of the first stage (510, 710, 810, 910); introducing the partially-treated liquid to an inlet of the second stage; measuring a total dissolved solids concentration and a flow rate of the partially treated liquid at the inlet of the second stage (510, 710, 810, 910); calculating a limiting current density for the second stage based in part on a measured total dissolved solids concentration of the partially-treated liquid and a measured flow rate of the partially-treated liquid; operating in the second stage (510, 710, 810, 910) at a second current density across the second cell stack, the second current density below the limiting current density for the second stage (510, 710, 810, 910) and lower than the current density of the first stage (510, 710, 810, 910); removing a second amount of total dissolved solids from the partially-treated liquid, in the second stage (510, 710, 810, 910), the second amount of total dissolved solids being less than the first amount of total dissolved solids to produce a treated liquid; wherein operating in the first stage (510, 710, 810, 910) further comprises operating at a first liquid flow velocity through the first stage (510, 710, 810, 910) and operating in the second stage (510, 710, 810, 910) comprises operating at a second liquid flow velocity through the second stage (510, 710, 810, 910), the second liquid flow velocity being greater than the first liquid flow velocity;