Nonindigenous species are introduced worldwide with ballast water (BW). To prevent further introductions, oceanic BW exchange and BW treatment systems are utilized, but their performance needs to be evaluated. To that aim, characterizing BW communities is essential but usually relies on exhaustive sampling and morphological taxonomic identification, which does not always allow fine-scale taxonomic resolution. Through the analysis of BW samples from 11 vessels arriving to the Chesapeake Bay (USA), we evaluated the potential of environmental DNA (eDNA) metabarcoding for BW monitoring by assessing whether the impact of BW management type could be identified, analyzing the influence of BW sampling access locations on communities, and comparing the accuracy of eDNA for taxonomic assignment and identification of nonindigenous taxa. We found that (1) different sampling access locations of the same tank resulted in different communities, (2) communities from treated and exchanged BW differ, (3) signals of source port and of ocean exchange are observed, (4) eDNA metabarcoding results in more diversity than morphological taxonomy, and (5) the nonindigenous copepod , not reported before in the Chesapeake Bay, is detected. Overall, this study highlights the potential of eDNA metabarcoding for BW monitoring, but more comprehensive sampling will be needed to optimize the approach.