Santurtzi has a very rough orography although excluding Mount Serantes (452m) - one of its most symbolic topographic elements, it is not at high altitude, the significant heights being spurs of the Serantes: The Mallet (245m) and the Fortified heights (123 and 106m). Its relief is within the north flank of the anticline of Biscay. It is a relief of a structural type corresponding to a series of materials of the Cretaceous period (limestone) throughout Punta Lucero-Serantes smoothly inclined towards the Estuary of Bilbao.

The climate in Santurtzi is of the humid oceanic climate type. The temperatures are moderate throughout the year, with more frequent rains in spring and autumn, winters are benign and summers not excessively warm.