A method for regeneration of cation and anion resins in an ion exchange water treatment system using a mixed bed separator with cation and anion resins with minimal cross-contamination, comprising: transporting the mixed resins from a working vessel to a separation/regeneration column, separating the anion resins from the cation resins using an upflow of backflush water, thus to divide the bed into two well stratified cation and anion layers, with the anion layer above, regenerating the anion resin layer by flowing a regenerating alkaline liquid down through the anion layer, and regenerating the cation resin layer by flowing a regenerating acid liquid up through the cation resin layer, while withdrawing the regenerating acid and alkaline liquids from the column essentially at an interface between the anion and cation layers, rinsing the respective regenerated layers with water, withdrawing essentially all of the anion resin layer from the column, leaving a small bottom portion of the anion resin layer remaining in the column, on top of the cation resin layer, withdrawing essentially all of the cation resin layer from the column, from a withdrawal level essentially at the bottom of the column, leaving a small portion of the cation resin layer remaining in the column, below the remaining anion portion, and leaving the small anion resin portion and the small cation portion to remain in the separation/regeneration column, to be mixed with a bed of cation and anion resins in a succeeding cycle of resin regeneration, wherein each of the anion and cation portions remaining in the separation/regeneration column is 15 to 20 cm deep, whereby the resins are regenerated with minimal cross contamination in a single separation/regeneration column. transporting the mixed resins from a working vessel to a separation/regeneration column, separating the anion resins from the cation resins using an upflow of backflush water, thus to divide the bed into two well stratified cation and anion layers, with the anion layer above, regenerating the anion resin layer by flowing a regenerating alkaline liquid down through the anion layer, and regenerating the cation resin layer by flowing a regenerating acid liquid up through the cation resin layer, while withdrawing the regenerating acid and alkaline liquids from the column essentially at an interface between the anion and cation layers, rinsing the respective regenerated layers with water, withdrawing essentially all of the anion resin layer from the column, leaving a small bottom portion of the anion resin layer remaining in the column, on top of the cation resin layer, withdrawing essentially all of the cation resin layer from the column, from a withdrawal level essentially at the bottom of the column, leaving a small portion of the cation resin layer remaining in the column, below the remaining anion portion, and leaving the small anion resin portion and the small cation portion to remain in the separation/regeneration column, to be mixed with a bed of cation and anion resins in a succeeding cycle of resin regeneration, wherein each of the anion and cation portions remaining in the separation/regeneration column is 15 to 20 cm deep, whereby the resins are regenerated with minimal cross contamination in a single separation/regeneration column.