Rapidly responding to incipient invasions is the most effective strategy to counter alien invasive species (AIS). Reliable monitoring programs defined by a high detection resolution and applicable on vast geographical and temporal scales are therefore a prerequisite for the development of successful extermination actions. Moreover, local abundance estimates can facilitate the design of effective region-scale management strategies by allowing resources to be allocated proportionally to the severity of the invasion. However, detecting aquatic biological invasions in an early stage and gauging the intensity of established invasions using conventional surveillance methods can be challenging, costly and destructive. In this study, we highlight the potential of environmental DNA (eDNA)-based species monitoring as the fundament of modern-day aquatic AIS management using the American bullfrog as a case study. This large frog species exerts a severe pressure on indigenous communities and is therefore ranked among the most destructive invaders worldwide. In Belgium, its distribution range covers 500 km² and in spite of almost a decade of intensive management efforts, successful eradication of this highly fertile and mobile species remains challenging. We first show how eDNA-based detection methods revealed the hitherto unnoticed expansion of a bullfrog population towards a new province. By quantifying eDNA concentrations before and after a national eradication campaign with droplet digital PCR (ddPCR), we then demonstrate that quantitative eDNA analyses can (i) accurately predict the number of bullfrogs that can be captured, (ii) locate breeding ponds that serve as dispersal hubs, (iii) evaluate the efficacy of eradication programs, and thus that this technique can be a valuable addition to the nature resource manager’s toolbox. As such, we present a novel approach in which quantitative eDNA analyses can significantly contribute to the control of biological invasions.