Gelling pointed out that the settlement is situated on an obvious ēg, i.e. an 'island' of dry land, projecting into the Humber Estuary, and surrounded on east and west by former marshy ground.

It is possible that Whitton was a landing stage on the south bank for the Roman fort and civitas of Petuaria Parisorum at Brough across the river.

[4][5] Pevsner states that the Church tower "re-uses massive blocks of Roman stone",[6] but these blocks of millstone grit which are to be found in several local churches (such as neighbouring Winteringham) may have been transported down the Ouse and the Humber from York where Roman buildings were being dismantled, or may even have come from some sort of triumphal arch or structure (perhaps like the Arch of Constantine), which might have stood at the end of Ermine Street.

The church was reseated in 1865 at the expense of Lady Strickland, and between about 1892 and 1897 the nave, chancel and roof were entirely rebuilt from the designs of W. & C. A. Bassett-Smith, architects, of London.

On the north side of the chancel are two stained-glass windows, erected in 1918 to the memory of Henry Spilman who was killed in the First World War.