Abstract Objective To categorise and map, at high resolution, the risk of malaria incidence in the Pacific region, the main malaria‐endemic region of Colombia. Methods The relationship between the environmental variables Normalized Difference Vegetation Index Normalized Difference Water Index, Topographic Wetness Index, precipitation and temperature with the observed Annual Parasitic Index was evaluated using a generalised linear model. An incidence risk map at a resolution of 1 km 2 was constructed and projected to the entire endemic region. Associations of malaria risk categories with both presence records and co‐occurrence of the three main malaria vectors were determined. Results A significant correlation was found for the incidence of malaria with precipitation and Normalized Difference Vegetation Index ( R 2 = 0.98, P < 0.05), whereas there was no significant correlation with the remaining environmental and topographic variables. Moderate‐ to high‐risk areas were located mainly in central Chocó Department along the San Juan and Atrato rivers and in areas west of the Cauca River and Pacific lowlands of the Andes Mountains. There was a statistically significant relationship for the presence of the two main vectors Anopheles darlingi and Anopheles nuneztovari with the high malaria risk category. Furthermore, malaria risk was directly proportional to the number of co‐occurring vector species. Conclusions The map obtained provides useful information on the risk of malaria in particular places of the Colombian Pacific region. The data can be used by public entities to optimise the allocation of economic resources for vector control interventions and surveillance.