In section II of this manual, we discussed polyphosphate's role as a cathodic corrosion inhibitor. However, in some applications, polyphosphate can be used effectively as a deposit control agent. Specifically, polyphosphates can function as threshold inhibitors to prevent the formation of calcium carbonate scale. While their use for this purpose is not usually applicable in open recirculating systems due to long retention times that can cause them to revert to orthophosphate, they can be used effectively as calcium carbonate stabilizers in once through systems.

Even more important is polyphosphate's ability to sequester iron and manganese thereby preventing their oxidation and resultant deposition. This application is particularly important in municipal water systems where the presence of iron or manganese can cause "red water" and "black water" problems, respectively. Unlike other deposit control agents that function via this mechanism, polyphosphate is one of the only ones approved for potable water.