The Cascade Steel Rolling Mill in McMinnville is an important shipper as well and propane shipments are handled by several distributors.

[1] Shortly after PNWR's startup, class one railroad Burlington Northern "spun off" part of its Oregon Electric Railway branch lines north of Salem to the new carrier.

[2] According to former WPRR/PNWR General Manager Robert I. Melbo, the Portland & Western was created to take over the new lines, rather than just extending the WPRR, due to regulatory issues then in force.

Most of the former SP branches are operated via a twenty-year lease agreement, which in the wake of the 1996 Union Pacific-Southern Pacific merger, are now held by UP.

Portland & Western became the "Operator" of the system while Willamette & Pacific remained in existence to retain ownership of assets.

In 2002, PNWR acquired a long-term lease of the remaining Burlington Northern branches in the state, giving the company access to Salem and Eugene via its own tracks.

The acquisition of the former allowed PNWR to make through movements from its Portland-area lines to its central yard at Albany without routing over the steep and curvy Rex Hill.

The first is the Albany and Eastern Railroad a subsidiary of the Rick Franklin Corp, which interchanges solely with the PNWR.

Although CORP and PNWR cross each other in Eugene, Oregon, operating agreements with Union Pacific prevented the two railroads from interchanging traffic directly.

Congestion problems experienced by UP in 2004 resulted in a new agreement allowing direct interchange, creating a new traffic flow on PNWR.

This line carried a significant number of carloads, primarily lumber, from Tillamook, Oregon, over the coast range via 100 miles of winding mountain railway.

A. Bruce Carswell resigned from the post in November 2008, replacing Larry Phipps, who retired in November 2005, who had replaced Robert I. Melbo who was WPRR/PNWR's first President and General Manager, having previously been the Superintendent of the Southern Pacific's Oregon Division which operated many of the lines before the WPRR was formed.

As of 2008[update], PNWR was operating run-through unit trains with grain from the BNSF to and from Port Westward on the Astoria Line west of Rainier.

[citation needed] In January 2025, a PNWR train derailed as the bridge trestle over the Marys River in Corvallis buckled.

Locomotives 1501, 1801, 1803, 1852 and 1854 were all retired from the PNWR and were originally meant to be scrapped by the railroad’s parent company Genesee and Wyoming as part of a fine resolution agreement with the EPA.

Begun in the 1990s and originally led by Washington County, the commuter-rail project was taken over by TriMet in 2002,[17] and the regional transit agency entered into an agreement with PNWR for the use of its right-of-way, and later for the operation of the rail cars.

Upgrades included a new roadbed, ballast, ties and rail to accommodate passenger train speeds of 60 MPH and freight train speeds of 40 MPH, Centralized Traffic Control signaling, Automatic Train Control at control points, new sidings, station platforms at the endpoints along with intermediate stations in Tigard, Oregon and Tualatin, Oregon, and in the Progress/Washington Square area near the Beaverton/Tigard city line, and a maintenance shop located in Wilsonville (staffed by TriMet employees).

TriMet also acquired two former Alaska Railroad Rail Diesel Cars, or RDCs, in late 2009 and refurbished them to serve as a backup train on occasions when one or more of the DMUs are out of service.

Cash passengers have the option in Tigard and Beaverton to first board a bus at the transit center to pay for cash and obtain a transfer which will be valid on the train; in Tualatin and at Hall/Nimbus bus service is infrequent to accommodate this, and TriMet does not serve Wilsonville and thus a passenger in Wilsonville wanting to pay a cash fare will simply not be permitted to board unless they purchase a prepaid ticket or pass online, or at the Wilsonville Fred Meyer (30300 SW Boones Ferry Road).