To prevent the worldwide spread of invasive aquatic species, the ballast water of ships may be disinfected with either physical or chemical treatment systems. Excess chemicals, such as chlorine, are neutralized before the ballast water can be discharged. Unfortunately, disinfection byproducts (DBPs) formed during treatment are not neutralized and remain potentially toxic. In this study, DBPs obtained from land-based tests of seven different ballast water treatment systems (BWTSs) have been statistically analyzed. Effect of operational factors (treatment type, holding time, source of carbon and active substance dosages) and environmental variables (salinity, pH, temperature, organic matter) were related to the formation of DBPs, such as trihalomethanes (THMs), haloacetic acids (HAAs), haloacetonitriles (HANs) and aldehydes. THMs and HAAs were the groups with major occurrences and concentrations detected in all BWTSs. Treatment type and source of carbon were the operational factors with major significance on DBP production, especially in chlorination systems. Salinity is the main variable determining DBP composition, as it differs between brominated-DBPs and chlorinated-DBPs. Concentration and type of organic matter (dissolved and particulate) have also a significant influence on the formation of total DBPs. According to the specific group of DBPs, some factors get significance. For instance, THMs are significantly affected by pH, and the production of aldehydes correlates positively with oxidant dose.