The unintentional release of aquatic nonindigenous species (NIS) via ballast water has long been recognized as a primary vector of biological invasions. To reduce the risk of ballast-mediated invasions, the International Maritime Organization (IMO) will direct ships to meet standards regarding the maximum number of viable organisms discharged in ballast water, with most ships expected to install ballast water management systems (BWMSs). Currently, filtration + ultraviolet (UV) irradiation is utilized as a common BWMS. There are issues, however, with enumerating viable phytoplankton after treatment at the low UV doses used onboard ships because the physiological effect occurs at the DNA level—organisms are reproductively sterilized but may remain alive for hours or days after treatment. The objective of this study is to examine three techniques to measure the number of viable phytoplankton cells following filtration + UV treatment: pulse amplitude modulation (PAM) fluorometry, epifluorescence microscopy using fluorescein diacetate (FDA) stain, and the serial dilution culture most probable number (MPN) method. PAM and staining techniques demonstrated similar patterns of phytoplankton reduction after UV irradiation. After 14 days, the MPN method confirmed viability of treated samples in enriched culture medium incubations and may be used to indicate potential recovery of damaged cells (i.e., “re-growth”). All cells that survived treatment and showed detectable growth after 14 days of incubation were smaller than 10 µm, as determined by microscopy. Combinations of direct and/or indirect measurements and culture-based methods might be the best solution to improve detection strategies and eliminate nonindigenous species.