Context Identifying the habitat preferences and core areas of Inia geoffrensis activity is essential to designing effective strategies for the management and conservation of Amazon River dolphins and their habitats in the Colombian Amazonas River and Orinoco basin. Objectives Quantify the differential use of habitat that Amazon River dolphins exhibit and identify core areas of activity during seasons of rising waters in the Colombian Amazonas River and five major rivers in the Orinoco basin. Methods Based on processed satellite images from Landsat 8 (2018–2021), we classified habitat types used by I. geoffrensis as reported in the literature as follows: (1) main river, (2) confluences, (3) tributaries, (4) channels, (5) islands, (6) bays, and (7) lagoons. We combined this dataset with GPS location data obtained from 17 tagged Amazon River dolphins to quantify the proportion of habitat types used. We used kernel density estimate (KDE) analysis to identify both areas used (K95) and core areas (K50) in the habitat types for the satellite-monitored individuals. Results Satellite tracking of I. geoffrensis individuals reported 16,098 locations classified into seven habitat types. For the analyzed period (rising waters) main habitat types used were as follow: (1) main river (n = 9144, 57%); (2) confluences (n = 932, 6%); (3) tributaries (n = 1423, 9%); (4) channels (n = 1597, 10%); (5) islands (n = 738, 5%); (6) bays (n = 1096, 7%), and (7) lagoons (n = 1168, 7%). Home range size (K95) for the satellite-monitored I. geoffrensis individuals ranged from 6 to 116 km2 (mean = 40 ± 33); and the largest core areas (K50) or core area of activity were recorded in the main river, confluences, channels, bays, lagoons, and tributaries. Conclusions Our results demonstrated the importance of spatial ecology analysis of Amazon River dolphins for the definition of protected areas, quantifying the use of ecosystems within these areas, and the location of priority areas for the implementation of management plans for the species and habitats.