The potential problems of organisms introduced by ballast water are well documented. In other settings, electrolytic generation of sodium hypochlorite from seawater has proven to be a simple and safe method of handling and injecting a biocide into water. After the hypochlorite oxidizes organisms, it reverts back to the chloride ion. Microcosm-scale testing of this technology combined with filtration, using organisms from Puget Sound, Washington, demonstrated that hypochlorite generation and use may be a viable method to eliminate aquatic nuisance species from ballast water while minimizing disinfection byproducts and residual toxicity. These experiments were conducted at the U.S. Geological Survey Marine Field Station on Marrow stone Island, Washington. Results from the first set of studies of the system showed that hypochlorite levels greater than 3.0 ppm hypochlorite with or without filtration reduced bacteria by more than 99.999%, reduced phytoplankton by more than 99%, and reduced mesozooplankton by more than 99%. Filtration improved efficacy only when hypochlorite concentration was initially less than 1.5 ppm.