Nonindigenous species (NIS) cause global biotic homogenization and extinctions, with commercial shipping being a leading vector for spread of aquatic NIS. To reduce transport of NIS by ships, regulations requiring ballast water exchange (BWE) have been implemented by numerous countries. BWE appears to effectively reduce risk for freshwater ports, but provides only moderate protection of marine ports. In the near future, ships may be required to undertake ballast water treatment (BWT) to meet numeric performance standards, and BWE may be phased out of use. However, there are concerns that BWT systems may not operate reliably in fresh or turbid water, or both. Consequently, it has been proposed that BWE could be used in combination with BWT to maximize the positive benefits of both management strategies for protection of freshwater ports. We compared the biological efficacy of "BWE plus BWT" against "BWT alone" at a ballast water treatment experimental test facility. Our comparative evaluation showed that even though BWT alone significantly reduced abundances of all tested organism groups except total heterotrophic bacteria, the BWE plus BWT strategy significantly reduced abundances for all groups and furthermore resulted in significantly lower abundances of most groups when compared to BWT alone. Our study clearly demonstrates potential benefits of combining BWE with BWT to reduce invasion risk of freshwater organisms transported in ships ballast water, and it should be of interest to policy makers and environmental managers.