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This study investigated the changes in concentrations of haloacetic acids (HAAs) and haloacetonitriles (HANs) as disinfection byproducts (DBPs) for different storage times (as long as 20 days) and temperatures (5 to 20°C). A ship's voyage after treatment of its ballast water with active substances was considered. The HAA showed a clear trend of increasing concentration only with storage time, especially for dibromoacetic acid (DBAA). Dissolved organic nitrogen concentration was increased by the decomposition of dead organisms at 10 days, and then reacted with the remaining total residual oxidants, resulting in increased concentration of DBPs. An environmental risk assessment indicated that DBAN and monochloroacetic acid (MCAA) could have a negative impact on the marine environment. This study suggests that, because all international vessels must have a ballast water management system installed by September, 2024, the concentrations of DBPs, especially DBAN, MCAA, and DBAA, should be monitored in the waters at major international ports.