The South Brooklyn Railway provides one of only two track connections between the New York City Subway and the rest of the American rail network. During the 1988 and 1999 reconstruction of the subway tracks on the Williamsburg Bridge, this connection allowed trains from the , and services, which were otherwise isolated during that period, to travel to Coney Island Yard for major work. At the other mainline rail connection at the Linden Shops, subway trains traveled via the Bay Ridge Branch of the Long Island Rail Road to the Brooklyn Army Terminal. From there, the at-grade New York Cross Harbor Railroad brought the cars up to the interchange yard at Second Avenue, where the South Brooklyn Railway took them to Coney Island Yard via the BMT West End Line.