In 1869 LIRR president Oliver Charlick wanted the branch to head off plans by the South Side Railroad to extend their line beyond Patchogue.
But Riverhead refused to pay the LIRR for the benefits of being at a junction, so the west end was moved to Manorville in the pine barrens in 1869.
During World War I, a freight spur was built onto the newly reinforced Long Wharf in Sag Harbor to deliver torpedoes for the E.W.
The freight house at the Sag Harbor train station housed the Sag Harbor Garden Center's retail store[6] until February 1, 2022, when renovations began to transform to building into Kidd Squid Brewing Company's flagship tasting room, which opened in July 2022 and continues in operation today.
In Eastport, the line ran beneath a bridge, which no longer exists, under Suffolk CR 51 then along the north end of Spadaro Airport, before merging with the Montauk Branch.