As chief engineer for the London City Council, his design feats included the first Blackwall Tunnel (1897) and Greenwich foot tunnel (1902) (both in Greenwich, London) and, further upstream, Vauxhall Bridge (1906).
By then knighted by Queen Victoria for services to engineering, he was elected President of the Institution of Civil Engineers in 1905.
He also designed, with Sir Benjamin Baker, major parts of London's drainage system, including east London sewage treatment works at Crossness and Barking on the south and north sides of the Thames respectively (these were sited at the ends of the sewer outfalls created by Sir Joseph Bazalgette during the late 19th century). Further afield, he also designed water works in Bradford, West Yorkshire.
Like several other notable engineers of the late 19th and early 20th centuries (eg: Sir William Halcrow, Sir Alexander Gibb), Binnie founded a firm under his name, which his son William took over on his father's retirement. in 1909 Sir Alexander Binnie and Son merged with another engineering consultancy to become Sir Alexander Binnie, Son & Deacon; later it became Binnie & Partners and from the 1990s it has been part of the multi-national Black & Veatch consultancy.