The switches at Kensington Junction were locked so that the branch was completely separated up to the Ninth Avenue & 20th Street Depot, which thereby became an unneeded facility because passenger streetcar operation had ended. At the same time, freight usage of the South Brooklyn Railway declined because of the increasing use of semi-trailer trucks. The McDonald Avenue trackage was no longer in use by 1978, and paved over by 1991. After the closure of the McDonald Avenue tracks, the South Brooklyn Railway's freight operations were moved from the Second Avenue yard to the 36th–38th Street Yard, where it still operates. In 1994, the last non-NYCTA customer on the line closed; the South Brooklyn Railway was then used almost exclusively for subway connections to the LIRR Bay Ridge Branch via the South Brooklyn Marine Terminal, Bush Terminal, and Industry City.
