St Mary's is a fragment of a priory of Cistercian nuns built in the late 12th century.
Wawne was originally Waghen. What little is known of the early history of Wawne church is contained in the mediaeval chronicle of Meaux Abbey. The founder, William de Gros, endowed the monks, before 1160, with land in Wawne, and also with the revenues of the church there, to mark his appreciation of the pioneer exertions of the monks in their first few years. In 1230 the Chancellor of York Minster acquired the church and retained it until the mid 19th century, when the rectorial rights passed to the Archbishop himself. The church in Sutton was a chapel subsidiary to Wawne church.
Among early endowments of Meaux Abbey were quarries at Hessle for chalk, and at Brantingham for stone. These building materials would be shipped up the river Hull to Wawne. The stone of Wawne church is of the same kind, and was no doubt quarried not far from the monks' pit.
Of the church existing on the 12th century nothing is visible except perhaps the cylindrical shafts of the nave piers and some square axe hewn Norman stones built into the west wall, as well as a carved head high up in the west wall, to the north of the west window. The chancel appears to date from 1230 when the church came into the possession of York.
One of the notable features of the church is the 5-light west window dating from the mid 15th century, also featuring rich perpendicular tracery; it is considered one of the finest in the country. The font is possibly from the Perpendicular period. It is lead-lined, and light areas show where new stone was inserted in the rim after the hasps and lock were forced open during the Reformation. The bell tower was heightened during the 15th century, and in mediaeval times there were four bells, now three. They were recast in 1874 but bear their origninal inscriptions and dates: 1629, 1632 and 1638. The only stained glass windows are in the south wall. They were placed there by a member of the Windham family, who were "lords of the manor" from about 1700 to the 1950s.