We conducted a shipboard ballast water test using seawater of extreme turbidity collected from Shanghai Port (China) (>300 mg total suspended solids (TSS)/L), and normal seawater collected in other ports (<100 mg TSS/L). All three types of International Maritime Organization (IMO)-approved ballast water management system (BWMS) tested failed to properly operate because of filter clogging or insufficient generation of oxidants under near-fresh water conditions with extremely high concentration of suspended solid during ballasting. It was also found that the number of microorganisms increased with longer ballast water retention time, with higher numbers in the treated discharge water. The results suggest that when operating a BWMS involving a filter unit in areas with water having high concentrations of suspended solids, the filter unit should be used during ballast water discharge, rather than during ballasting. This method has the advantage of removing ≥50 µm organisms at discharge that could not be removed by a filter during ballasting. For ballast water retained for long storage times, the results suggest the use of BWMSs involving UV units or electrolysis during deballasting. In addition, BWMSs involving electrolysis units provide the opportunity to maintain residual total residual oxidant (TRO) levels, using a partial ballast tank. Although the BWMSs tested are a small subset of the large number of IMO-approved BWMSs, the results demonstrate that there is a significant gap between the technology currently available and capacity to meet IMO and US Coast Guard standards.