The watershed management area includes watersheds draining the northern coastal plain of New Jersey. The area lies in parts of Hunterdon, Somerset, Middlesex, Mercer and Monmouth Counties and includes the following principal watersheds: Millstone River, Stony Brook and Bedens Brook.

The Millstone River drains an area of 271 square miles, including parts of Hunterdon, Somerset, Middlesex, Mercer and Monmouth Counties. This river is 38 miles long and flows from Millstone Township in Monmouth County to the Raritan River near Manville and Bound Brook. 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. The pattern for inorganic nitrogen is different, moderate (but acceptable) near Manalapan, very high at Grovers Mill, and lower again 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. Landfills are assessed as problems, both in the upper watershed where recreational usage and ground water are impacted and in South Brunswick where leachate from a municipal landfill has been noted by local authorities as a problem.