The highest point in Upton is above sea level, just off the junction with the A551 and the B5139, at Moreton Road, in the centre of the village. A further prominence of above sea level is at Upton Manor, from the centre of the village. Most of the populated area is more than above sea level, and most of the ground is on a gentle hillside. Consequently, Upton has avoided the significant flooding which can happen in the nearby low-lying Fender valley. Due to its inland location and elevation Upton is not prone to coastal flooding, which can happen at West Kirby, Hoylake, Meols and New Brighton.