The parish of Winterbourne Stoke mostly consists of downland, with chalk outcrops in places. It is bisected from north to south by the River Till, which rises to the north on Salisbury Plain, and which was originally called the River Winterbourne. The village is located at the junction of the B3083, running north and south, and the A303 trunk road, running east and west. The land is gently sloping; level areas near the river have been used as meadowland and slightly sloping land for arable cropping since the Middle Ages.
Especially in its east part, the parish is rich in archaeological remains. The Greater and Lesser Cursus are Neolithic monuments, and there are a group of seventeen long barrows, some of which are in neighbouring parishes. A Romano-British settlement has been identified on Winterbourne Stoke Down, as well as some medieval earthworks. Most of the Parsonage Down national nature reserve is within the parish. This ancient downland is rich in wild flowers as well as having scrubby areas where yellowhammers and turtle doves flourish.