There are direct operating trains such as higher-category train, Special Rapid and Rapid train (running as a local train within the Biwako Line) that run from the JR Kyoto Line and JR Kobe Line.
優等列車のほか、新快速や快速列車（琵琶湖線内では普通列車）がJR京都線・JR神戸線から直通運転している。