On July 1, 1892, the New York, New Haven and Hartford Railroad leased the Housatonic, forming the Berkshire Division; it was merged on March 29, 1898.

The main line was also gone between Brookfield and Hawleyville, with traffic using the branch to Danbury and old New York and New England Railroad.

Excursion trains began operating between Canaan and just south of Cornwall Bridge (at Belsprings Siding) in November 1984.

In April the Housatonic began to serve Becton, Dickinson and Company, a plastics plant in Canaan, but almost immediately the line was severed at Falls Village by a washout, not repaired until 14 months later.

That month the Housatonic bought the connecting Guilford trackage (Canaan Running Track) north to Pittsfield, Massachusetts, where it obtained another interchange with Conrail.

In December 1992, the Danbury Terminal Railroad acquired trackage and rights belonging to Conrail in southwestern Connecticut and southeastern New York.

A few freight shipments were forwarded from Danbury by Metro-North crews, but this arrangement was only temporary until the remaining customers converted to truck transportation.

In 1984, the Berkshire Scenic Railway Museum began operating passenger excursions between Lee and Great Barrington, over tracks owned by the Housatonic Railroad.

The excursion trains returned in 2003, based out of the restored station in Lenox, with regular schedules to Lee and Stockbridge.

In 2008 HRRC considering the possibility of resuming commercial passenger service along the entire line from Danbury to Pittsfield, and in May 2010 began a formal study of the same.

Colin Pease, spokesperson for HRRC, said, "The Housatonic Railroad has determined that the continued operation of the Berkshire Scenic Railway on Housatonic-owned tracks is no longer possible."

In July 2014, Massachusetts Department of Transportation's Board of Directors authorized the purchase of 37 miles of the railroad's Berkshire Line.

[4] On October 14, 2020, a HRRC employee was fatally struck by a maintenance of way vehicle while working in North Canaan, CT, prompting an investigation by the National Transportation Safety Board.