Biofouling is a major vector in the transfer of non-native species around the world. Species can be transported on virtually all submerged areas on ships (e.g. hulls, sea-chests, propellers) and so antifouling systems are used to reduce fouling. However, with increased regulation of biocides used in antifoulants (e.g. the International Maritime Organization tributyltin ban in 2008), there is a need to find efficient and sustainable alternatives. Here, we tested the hypothesis that short doses of low salinity water could be used to kill fouling species in sea-chests. Settlement panels were suspended at 1.5 m depth in a Plymouth marina for 24 months by which time they had developed mature biofouling assemblages. We exposed these panels to three different salinities (7 psu, 20 psu and 33 psu) for two hours using a model sea chest placed in the marina and flushed with freshwater. Fouling organism diversity and abundance was assessed before panels were treated, immediately after treatment, and then one week and one month later. Some native ascidian <i>Dendrodoa grossularia</i> survived, but all other macrobenthos were killed by the 7 PSU treatment after one week. The 20 PSU treatment was not effective at killing the majority of fouling organisms. On the basis of these results we propose that sea-chests be flushed with freshwater for at least two hours before ships leave port. This would not cause unnecessary delays or costs and could be a major step forwards in improving biosecurity.