Waterbird populations are rapidly declining worldwide, including in many countries in Southeast Asia. Massive land use changes in Peninsular Malaysia are a major threat to biodiversity due to habitat loss and alteration, affecting the populations of many waterbird species. This study was conducted to determine the spatial distribution of three stork species, the Asian Openbill Anastomus oscitans, Painted Stork Mycteria leucocephala and Milky Stork Mycteria cinerea, in Peninsular Malaysia using the citizen science database, eBird. About 86,881 occurrences of the Asian Openbill, 2,391 occurrences of the Painted Stork and 242 occurrences of the Milky Stork were identified in the eBird database throughout Peninsular Malaysia between 2019 and 2021, suggesting major differences in occurrence size between the three species. Map generated from ArcGIS and a statistically significant difference in the population distribution of the three stork species across Peninsular Malaysia indicate habitat segregation. The populations of these stork species should be carefully monitored and managed to avoid imbalance with other waterbird populations.