To meet the strict requirements of reducing sulfur emission, more and more commercial ships have installed exhaust gas cleaning systems (EGCSs). However, wash water produced during cleaning process is discharged back to the marine environment. We investigated effects of the closed-loop scrubber (natrium-alkali method) wash water on three trophic species. Severe toxic effects were found when Dunaliella salina, Mysidopsis bahia and Mugilogobius chulae were exposed to 0.63-6.25, 0.63-10 and 1.25-20% concentrations of wash water, respectively. EC50-96 h of D. salina was 2.48%, corresponding to total polycyclic aromatic hydrocarbons (PAHs) or heavy metals were 22.81, 23.67 µg L−1. LC50-7 d of M. bahia and M. chulae were 3.57 and 20.50%. The LOEC of M. bahia and M. chulae were 1.25% and 2.5%, corresponding to total PAHs and heavy metals were 11.50, 11.93 and 22.99, 23.86 µg L−1. M. bahia’s body weight was negatively correlated with concentrations of wash water. Although wash water contained high concentrations of PAHs (e.g., naphthalene) and heavy metals (e.g., Cr, Ni, Cu and Zn), none of the single pollutant could explain the high toxicity of wash water. The measured toxicity might arise from synergistic effects among several contaminants or from other more toxic contaminants we know very little about. We highly recommend that wash water should be treated prior to being discharged to the marine environment.