To reduce the spread of aquatic invasive species, the discharge of ballast water by ships will soon be compulsorily regulated by the International Maritime Organization (IMO) and the United States Coast Guard (USCG). Compliance with their regulations will have to be achieved by onboard ballast water management systems. To monitor the treatment system performance, rapid and easy compliance techniques are required. This paper reports on the suitability of adenosine triphosphate (ATP) to quantify living 10–50-μm organisms at −1, which is the upper limit of the IMO D-2 and USCG regulations. Initial tests revealed that commercially available ATP assays lacked sufficient sensitivity to monitor ATP in treated ballast water. A rapid and easy concentration method was developed to increase sensitivity and remove interfering salts, non-target organisms (Micromonas pusilla), and dissolved ATP. Laboratory experiments revealed that salinity was reduced 33 times and concentration efficiencies reached 85 %. The ATP assay was tested in a UV-based full-scale ballast water management system, treating seawater and fresh water. ATP levels were compared with two alternative compliance tools: fluorescein diacetate (FDA) and Photosystem II efficiency. Results showed a 10-fold decrease in ATP levels after treatment compared to a 5-fold decrease in alternative compliance techniques. Following refinements, the ATP assay’s detection limit reached 2.5 ± 0.5 cells mL−1 using a Thalassiosira rotula monoculture. Initial estimates of the pass and fail level were 50 and 6000 relative luminescence units, respectively. Further validation is recommended. The ATP assay is a promising tool for ballast water compliance testing.