Any treatment process used to render ballast water safe for discharge creates some form of residual. If chemical biocides are used, either chemical residuals or reaction byproducts will be generated. If a physical separation process, such as filtration, is used, the material collected from suspension must be discharged. If waste engine heat is used to heat ballast water, the temperature of the discharged ballast water will be substantially higher than the ambient water. All of these factors must be considered when developing a treatment plan.

Treatment with biocides may be of concern because the residual biocide in the water that is discharged into a harbor could be toxic to local organisms. Although residual biocides could have lethal effects if present in high concentrations in the immediate vicinity of a ship using biocidal ballast water treatment, they also could have deleterious sublethal effects on organisms further away. In addition to concerns about the biocide itself, treating water that contains organic materials can result in the formation of a variety of organohalogen molecules. Some of these, such as trihalomethanes, can be mutagenic and carcinogenic, as well as persistent in the environment; others with low water solubility are likely to accumulate in bottom sediment and could become a source for bioaccumulation of toxic chemicals in the local aquatic food web.

Release of heated water from ballast tanks may be of environmental concern because the hot water would be lethal to organisms living immediately near the vessel. Organisms located further away would not encounter lethal temperatures but would, nevertheless, be subjected to additional stress and elevated oxygen requirements; at the same time, available oxygen would be reduced because warm water holds less oxygen than cold water. Thermal releases from ships are not currently regulated, although other sources are controlled. Legislation related to thermal releases is directed primarily at power plants that use local water to cool their machinery and continually release heated water back into a river or estuary. The continuous releases from power plants are a much greater source of heated water than sporadic discharges from ships using thermal ballast water treatment. Furthermore, if ships heated their ballast water during the initial days of a voyage, the water would probably have cooled by the time it was discharged; therefore it would have even less environmental impact.

Perhaps the most environmentally benign discharge from a system for treating ballast water consists of suspended solids washed from filters. Material released from periodically backflushing a media filter or continuously washing a membrane filter is a more concentrated version of what was originally in the local water (planktonic organisms and suspended sediment particles). The nature and concentration of materials in the backflush are predictable and would need to be evaluated only in areas of known contamination. The return of these constituents to the water at their site of origin should be of environmental concern only when toxicity has been defined.

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