Upton lies at the geographic centre of the northern part of the Wirral Peninsula, from the Irish Sea at Leasowe Lighthouse, north-east of the Dee Estuary and a similar distance south-west of the River Mersey. Upton sits on a low-lying hill, in a wide and shallow glacial U-shaped valley, formed during the Quaternary Ice Age, between Bidston Hill and Thurstaston Hill. The underlying bedrock is Triassic bunter sandstone of the Helsby Sandstone Formation and the Sidmouth Mudstone Formation. This is overlain with boulder clay from the Quaternary Ice Age, similar to the nearby Dee Cliffs, and clay soil. The bedrock is not usually visible, as it is on the nearby Bidston Hill.