In recent years, the issue of invasive alien species brought on by ballast water has drawn increasing attention, and advances in ballast water treatment technologies have been made. One of the most popular combined ballast water treatment technologies utilized in ballast water management systems (BWMSs) globally is filtration + UV-C radiation. During the actual voyage of the ship, ballast water is treated by the BWMS and then enters the dark ballast tanks until the ballast water is discharged. Marine organisms are able to complete DNA damage caused by UV radiation in dark ballast tanks. Therefore, the length of holding time affects the effectiveness of the BWMS in treating ballast water. The objective of this study was to examine the efficacy of filtration + UV-C irradiation treatment at different holding times for the removal or inactivation of phytoplankton and zooplankton populations during simulated ballast water treatment. Results indicate that the holding time after the filtration + UV-C radiation treatment increased the inactivating efficacy, especially for zooplankton in natural seawater. For phytoplanktons in ballast water, the strongest impact on the treatment efficacy was reached with a holding time of 24 h.