Santa Gertrudis is located in the geografical centre of the island and is one of the three parishes in Ibiza that does not look out to sea. Most of the area is located between 100 and 300 metres above sea level. The highest point is Sa Torreta (344 m). Most of this land dates back to the Quaternary period, which began 2.59 million years ago and continues today. It was at the beginning of this era that Homo Sapiens appeared on the Earth and that large species of plants and animals became extinct. 

A considerable amount of Santa Gertrudis municipality is farmland. In the lower areas, the presence of oleander indicates damp soils. The reddish, deep soil of the plains has few stones and is very fertile. In contrast, the whiter soil in higher stonier places is covered by forest and is less productive for farming. There are mastic shrubs, junipers, heather, rosemary, broom, almond and carob trees, while a blanket of poppies colours the fields in Springtime. 

The Santa Eulària river is the largest river basin on the island and runs through Santa Gertrudis from Northwest to Southeast, creating important underground waterways. In this area there are also some more streams, canals and brooks, wells and waterwheels. At one point there were up to twenty water reservoirs which were small dams that elevated the water level and channeled it to irrigate considerably large farmlands. Very close to the church there is also a well. In fact, it was decided to build the church where there was an abundant fountain, and dedicate it to the virgin of Santa Gertrudis.