In its lower (southern) portion, it flows through the most urbanized and industrialized areas of the state, including along Downtown Newark.

Leaving Dubourg Pond the river travels northeast and crosses Corey Lane before entering the Buck Hill Tract Natural Area.

However At this point, the river begins to generally flow south, through Morristown National Historical Park, and forms the boundary between Morris and Somerset counties.

The river passes through a gorge in Millington and then turns abruptly northeast, flowing through the valley between Long Hill to the west and the Second Watchung Mountain to the east.

Southwest of Lincoln Park it passes through the Great Piece Meadows, where it turns abruptly eastward and is joined at Two Bridges by its major tributary, the Pompton River, then meandering through Little Falls, New Jersey as it drops over a fall, across some rapids, and under Passaic County Route 646 and an abandoned railroad trestle.

[7] Proceeding beyond the Wallington Reach, the river remains navigable via a series of maintained channels to its final destination, Newark Bay.

It passes Passaic, Clifton again, then Nutley and Belleville on the west; it flows past Rutherford, Lyndhurst, and North Arlington to the east.

The Passaic River found a new path to the ocean via the Millington Gorge and the Paterson Falls as the glacier that covered the area retreated northward and the lake drained.

Prior to European colonialization along the Passaic in the late 17th century, the valley was the territory of the Lenape groups now known as the Acquackanonk and Hackensack, who used the river for fishing.

It provided a navigable route connected by canals to the Delaware River starting in the late 18th century.

In 2008, the EPA reached a settlement with Occidental Chemical Corporation and Tierra Solutions Inc. to clean a portion of the polluted river.

A New Jersey Superior Court judge, ruling in July and September 2011, stated that Occidental and Maxus Exergy Corporation (a subsidiary of YPF) are liable for remediation in other portions of the river.

[9] In 2013, several corporate defendants agreed to pay the State of New Jersey $130 million for ecological damages related to Passaic River pollution.

[12] In April 2014 EPA announced a $1.7 billion plan to remove 4.3 million cubic yards (3.3×10^6 m3) of toxic mud from the bottom of lower eight miles (13 km) of the river.

[4] The decline of manufacturing on the lower river has left a post-industrial landscape of abandoned and disused factories and other facilities.

Innovation Fuels LLC, one of the terminal's tenants, has plans to continue to sell two barge loads a month of biodiesel to customers in Europe.

Although they experienced some delays with the County drawbridges that have been neglected for years and had some problems with shoaling due to the lack of maintenance dredging, they remain undeterred and the Passaic River represents the cheapest and most efficient method to ship their cargo to its customers.

As part of the ongoing Newark revitalization effort by the city government, parkland is proposed along the banks of the river.

On April 23, 2010, Governor Chris Christie issued an order creating the Passaic River Basin Flood Advisory Commission.

From 2006 to 2008, writer Wheeler Antabanez traveled the Passaic River and its shores, chronicling his adventures in a special issue of Weird NJ magazine.