Malaria is one of the most cited vector-borne infectious diseases by climate change expert panels. Malaria vectors often need water sheets or wetlands to complete the disease life cycle. The current context of population mobility and global change requires detailed monitoring and surveillance of malaria in all countries. This study analysed the spatiotemporal distribution of death and illness cases caused by autochthonous and imported malaria in Spain during the 20th and 21st centuries using multidisciplinary sources, Geographic Information System (GIS) and geovisualisation. The results obtained reveal that, in the 20th and 21st centuries, malaria has not had a homogeneous spatial distribution. Between 1916 and 1930, 77% of deaths from autochthonous malaria were concentrated in only 20% of Spanish provinces; in 1932, 88% of patients treated in anti-malarial dispensaries were concentrated in these same provinces. These last data reveal the huge potential that anti-malarial dispensaries could have as a tool to reconstruct historical epidemiology. Spanish autochthonous malaria has presented epidemic upsurge episodes, especially those of 1917–1922 and 1939–1944, influenced by armed conflict, population movement and damaged health and hygiene conditions. Although meteorological variables have not played a key role in these epidemic episodes, they contributed by providing suitable conditions for their intensification. After the eradication of autochthonous malaria in 1961, imported malaria cases began to be detected in 1973, reaching more than 700 cases per year at the end of the second decade of the 21st century. Therefore, consistent and detailed historical studies are necessary to better understand the drivers that have led to the decline and elimination of malaria in Europe and other temperate countries.