The spread of aquatic invasive species through ballast water is a major ecological and economical threat. Because of this, the International Maritime Organization (IMO) set limits to the concentrations of organisms allowed in ballast water. To meet these limits, ballast water treatment systems (BWTSs) were developed. The main techniques used for ballast water treatment are ultraviolet (UV) radiation and electrochlorination (EC). In this study, phytoplankton regrowth after treatment was followed for six BWTSs. Natural plankton communities were treated and incubated for 20 days. Growth, photosystem II efficiency and species composition were followed. The three UV systems all showed similar patterns of decrease in phytoplankton concentrations followed by regrowth. The two EC and the chlorine dioxide systems showed comparable results. However, UV- and chlorine-based treatment systems showed significantly different responses. Overall, all BWTSs reduced phytoplankton concentrations to below the IMO limits, which represents a reduced risk of aquatic invasions through ballast water.