B

• Bay Ridge Line
• Bath Beach and Bensonhurst Line to Ulmer Park
• Brighton Beach Line
• Bergen Beach Line
• Bowery Bay Line
• Broadway Line
• Broadway and Jamaica Avenue Line
• Brooklyn Hills Line
• Bushwick-Meeker Line
• Bushwick Avenue Line

C

• Calvary Cemetery Line
• Corona Line
• Court Street Line
• Crosstown Line
• Coney Island and Brighton Beach Line
• Cypress Hills Line
• Cypress Hills Extension

E

• East New York Line

F

• Flatbush Avenue Line
• Flushing Avenue Line
• Forest Park Line
• Fort Hamilton Line
• Fresh Pond Line
• Fulton Street Line
• Furman Street Line

G

• Gates Avenue Line
• Glendale Line
• Graham Avenue Line
• Grand Street Line
• Greene and Gates Avenues Line
• Greenpoint Line
• Greenpoint Line

H

• Hamilton Avenue Line
• Holy Cross Cemetery Line

J

• Jamaica Line

K

• Kingston Avenue Line

L

• Lorimer Street Line
• Lutheran Cemetery Line

M

• Manhattan and Nassau Avenues Line
• Meeker Avenue Line
• Meeker Street Line
• Metropolitan Avenue Line
• Montague Street Line
• Myrtle Avenue Line

N

• Nassau Avenue Line
• Nostrand Avenue Line

P

• Putnam Avenue Line
• Putnam Avenue and Halsey Street Line

R

• Reid Avenue Line
• Ralph Avenue Line
• Richmond Hill and Jamaica Line
• Ridgewood Line

S

• Sea Beach Line to Coney Island
• Second Avenue Line
• Sumner Avenue Line

T

• Third Avenue Line to Fort Hamilton and Bensonhurst
• Tompkins Avenue Line

U

• Union Avenue Line
• Utica Avenue Line

The railroad also partially owned the Bridge Operating Company, a line across the Williamsburg Bridge that was also owned by New York Railways.