The population centers in this drainage basin are Princeton Township and Borough, Manville, South Brunswick Township, East and West Windsor Townships, Hightstown and Pennington Boroughs. The land use in the Millstone watershed is primarily suburban development with scattered agricultural areas. Extensive and recent development is present in the Upper Millstone watershed. Nutrient enrichment, as reflected in total phosphorus, varies in the Millstone from mild as observed near Manalapan, to severe downstream at Blackwells Mill. Grovers Mill shows severely depressed dissolved oxygen in the summer and fall.
Elevated lead appears to be a problem at all three monitoring locations.
In addition, violations were recorded near Manalapan for zinc and at Grovers Mill for cadmium. Sediments, nutrients, and pesticides are suspected of coming from croplands, and are believed to be severe in the East Windsor area where chronic fish kills have occurred in the past. It is a combination of agricultural and urban runoff that is suspected of degrading the fish communities in the upper Millstone River. Other nonpoint pollution sources have been reported in the Millstone watershed. Fuel oil spills have occurred in the Upper Millstone, causing fish kills.