In the era of globalization, biological invasions are one of the most serious social issues. Thus, managing its impact is an urgent task. It is essential to control non-native species before they become established. However, it is insufficient to address establishment debt, which occurs when a non-native species has been introduced into an area but has not yet been established in the wild. In particular, unintentionally introduced or contaminated organisms of the aquatic ornamental pet trade are referred to as “hitchhikers” and have not received much attention in the context of establishment debt. To understand the nature of establishment debt, including that of aquatic hitchhikers, I propose the monitoring of non-native species inhabiting artificial isolated waters, such as indoor aquariums, and the construction of a database using environmental DNA metabarcoding. This idea would be an effective non-regulatory management approach when implemented broadly, at the country level. Furthermore, implementation of this strategy in combination with border biosecurity and field monitoring may promote accurate prioritization, rapid species identification, and effective invasion pathway assessment.