A method of and system for removing phosphorus from wastewater using a waste sludge that has a high affinity for phosphorus. In order for the waste sludge to be used in a flow-through contact reactor to remove the phosphorus from a wastewater stream, the waste sludge is pelletized. The waste sludge pellets are packed into one or more flow-through contact reactors. In the configuration described herein, phosphorus removal is maximized by flowing the wastewater through the reactor(s) in a "pulsed" manner, rather than continuously. Thus, wastewater is flowed through the reactor(s) for a period of time and stopped for a period of time. By giving the sludge absorbant a rest period, the absorption capacity of the sludge is increased significantly, thus decreasing the frequency of regeneration or replacement of the sludge. Sludge regeneration can be accomplished with a stripping step using an alkaline solution of pH 13, followed by rinsing with water.