Mungia lies 20 metres above sea level in an area full of open spaces, with a landscape of rolling hills; among these last are Gondramendi (217 m), Tallu (342 m) and Berreaga (366 m). The more important mountains nearby are Sollube (684 m) and Jata (592 m); these surround the valley of the Butroi river, which rises at the mountain of Bizkargi (536 m) and flows to the sea at the Plentzia estuary.

There are many small streams and underground springs, such as the Atxuri, Trobika, Lauromendi, Atebarri, or Mantzorriko Erreka, which are all tributaries of the Butroi river and provide water to the numerous fountains built in the town. In the past those waters helped to run more than 20 mills, some of which are still standing today.