The transfer of ship ballast water poses significant risks to the aquatic ecosystem and human health. To mitigate the influences of non-native species, ballast water management systems (BWMS) have been installed on international ships to ensure proper treatment of ballast water before discharge. This study investigates whether ballast water discharges managed by BWMS meet the requirements of the D-2 standard for organisms in different size classes. Representative ballast water samples were collected from 28 ships (a total of 20 different BWMS) arriving in Shanghai during the period 2020–2022. Results have shown that two samples (7.1 %) exceeded the D-2 Standard. The compliance rates varied among different vessel types, with cargo vessels achieving a compliance rate of 81.8 %, while LNG vessels and container vessels achieved 100 % compliance. The potential to achieve higher levels of ballast water management will increase as crews improve their skills in operating BWMS and BWMS is further developed. •Investigate ballast water from Cargo, LNG, and Container to determine compliance with the D-2 standard.•The compliance with the D-2 standard for ballast water after treatment on different ship types is different.•Non-compliant samples with ≥ 50 um living organisms had the lowest compliance rate with the D-2 standard.•The study reveals that non-compliance with the D-2 standard is mainly due to misuse of ballast water management systems.