A multi-stage water conditioning system is structured for conditioning a flow of influent water passing through the conditioning system by removing one or more cations including sodium, iron, barium, and or ammonia from the influent water, while also possibly adding (as required) calcium and magnesium. Such a conditioning of the influent water results in a reduction in the sodium adsorption ration (SAR) and electrical conductance (EC) of the influent. Versions of the water conditioning system may include a surge and equalization stage, and at least one conditioning stage, which is typically followed by an output finishing stage. Each included conditioning stage provides for a contacting of the influent water with surfaces of a load of molecular filtering material causing a reduction in sodium and other cations as the influent waters flow through the water conditioning system. The system further provides for the inclusion of a regeneration mechanism that is included for regenerating each load of molecular filtering material of each conditioning stage when the molecular filtering material becomes saturated with cations such as sodium, barium, and iron, which have been removed from influent water being conditioned.