On returning to England the same year, he again considered Holy Orders but instead was attracted to Manchester to join the chemical laboratory of Lyon Playfair at the Royal Manchester Institution. Here he became involved in some of the environmental issues of the worlds first industrial city (see History of Manchester). Playfair left for greener pastures in 1845 and Smith worked at making a living as an independent analytical chemist. After some initial alarming experiences, Smith refused to take on expert witness work which was a staple of consulting scientists of the day and which he saw as corrupt. Consequently, when the Alkali Inspectorate was established by the Alkali Act 1863, Smiths integrity made him the natural candidate. As Queen Victorias Inspector of Alkali Works, he was the prototype of the scientific civil servant. He held the post until his death. He is buried in the graveyard of St Pauls Church on Kersal Moor, Salford
In 1872 Smith published the book Air and Rain: The Beginnings of a Chemical Climatology, which presents his studies of the chemistry of atmospheric precipitation. These studies include the discovery, in 1852, of acid rain in northern British cities, a consequence of the burning of coal rich in sulfur. He was conferred with Honorary Membership of the Institution of Engineers and Shipbuilders in Scotland in 1884. After his death his collection of about 4,000 books was acquired by the library of Owens College, Manchester. They are now in the John Rylands University Library, the successor of the college library.