Ship's ballast waters transport large numbers of organisms which may become invasive in coastal regions. One option to address this problem is the use of biocides as ballast water treatment (BWT). Efficacy and environmental acceptability of three commercial active substances (the BWT biocides Peraclean® Ocean and Seakleen®, and alkylamine-based biocide Mexel® 432/336) were tested against three bacteria species, two vegetative microalgae and one zooplanktonic larva, in 10 and 30 Practical Salinity Unit (PSU) waters. In both salinities, PeraClean® Ocean was the most effective biocide against bacteria causing > 90% mortality at 20 mg/l, compared with 50 mg/l for Mexel® 432/336 and > 500 mg/l for Seakleen®. Regarding zooplankton, Seakleen® was the most effective chemical causing 90% mortality in 24 h at concentrations < 6 mg/l (LC9024 h) in both salinities, compared with 23 and 26 mg/l for Mexel® 432/336 and 370 and 480 mg/l for PeraClean® Ocean in 10 and 30 PSU, respectively. Similar pattern of efficacy was obtained for microalgae in 30 PSU: effective concentrations inducing 50% growth inhibition in 4 days were ≤ 1.6 mg/l for Seakleen®, ≤ 10.1 mg/l for Mexel® 432/336 and ≤ 30.9 mg/l for PeraClean® Ocean. Our work highlighted that treated waters displayed residual toxicity after 24 h still inducing mortality depending on the organism and biocide. However Mexel® 432/336 is the only biocide which had no impact on oyster larvae development at effective concentration. Altogether our data showed that Mexel® 432/336 was the only biocide displaying a broad spectrum efficacy in concentrations < 50 mg/l and not toxic for oyster larvae development at this concentration. However residual toxicity of treated waters for any organism should be taken into account in BWT systems utilising biocides.