Is WaterGEMS/WaterCAD capable of modeling the formation of constituents in networks?
This should be possible. You would need to formulate a constituent that has a positive bulk or wall decay rate and, if appropriate, an equilibrium concentration. A quick test with artificial reaction rates in a test model will show a growth of a generic constituent along a series of pipes.
For the input for this, you would need to do field testing to develop these actual reaction rates. This is the difficult part of this type of modeling. Values such as bulk reaction rate and wall reaction coefficients are highly dependent upon your system and are generally determined experimentally.