Having had several former name variants, including "Markyate Street" and "Mergyate", Markyate has been part of one or other of the three counties of Hertfordshire, Bedfordshire and Buckinghamshire at various times, as the county boundaries have changed over the years. At one time the boundary was the line of the main road itself: Hertfordshire to the east and Bedfordshire to the west. Markyate is close to the source of the River Ver, which has occasionally flooded the centre of the village, though the watercourse is often dry during parts of the year.