Primary freshwater crabs represent a culturally and ecologically significant component of freshwater habitats globally that has a high percentage of threatened species. Invasive species (especially non-indigenous crayfish) and climate change are not only important standalone threats, but are also expected to compound existing threats (e.g., habitat loss/modification, pollution) and challenge the long-term survival of these decapod crustaceans. This study illustrates the importance of considering these two emerging and growing threats in conservation or management strategies by quantifying (via species distribution models) the individual and aggregated risks of these threats in Southeast Asia, a region with the highest diversity of primary freshwater crabs and a high proportion of imperiled species. Results predicted that most species of crabs (82.1%) will co-occur (and hence interact) with invasive crayfish to a moderate to high degree, and most species (69.2%) will also experience a reduction in suitable climate conditions in the future. In terms of aggregated risk, the results also predict an increased overlap between invasive crayfish and native crabs for three out of the seven species analyzed (namely Procambarus virginalis, Cherax destructor and Orconectes rusticus). Findings from this study provide a quantitatively derived rationale for the development of adaptive regulations and conservation plans in the region to minimize the risk of invasive species in a cost-effective way, thereby enabling the protection of Southeast Asia's natural heritage and its vital ecosystem services.