Biological invasions are a human-induced environmental disturbance that can cause major changes in ecosystem structure and functioning. Located in the northeastern Mediterranean basin, the Aegean Sea is a hotspot of biological invasions. Although the presence of alien species in the Aegean has been studied and monitored, no assessment has been conducted on their cumulative impacts on native biodiversity. To address this gap, we applied the CIMPAL index, a framework developed for mapping the cumulative impacts of invasive species, to identify the most affected areas and habitat types and determine the most invasive species in the region. Coastal areas showed stronger impacts than the open sea. The highest CIMPAL scores were four times more frequent in the South than in the North Aegean. Shallow (0–60 m) hard substrates were the most heavily impacted habitat type, followed by shallow soft substrates and seagrass meadows. We identified Caulerpa cylindracea, Lophocladia lallemandii, Siganus luridus, Siganus rivulatus, and Womersleyella setacea as the most impactful species across their range of occurrence in the Aegean but rankings varied depending on the habitat type and impact indicator applied. Our assessment can support marine managers in prioritizing decisions and actions to control biological invasions and mitigate their impacts.