Exotic invasive species in the Gippsland Lakes are aquatic pest animals that compete with native species for resources, such as food and habitat (e.g. the Mediterranean fan worm and European shore crab), or prey on native animals including fish larvae, and native fish and frog eggs (e.g. the eastern gambusia and northern Pacific seastar).
Other species include the European carp which damage the benthic environment and make the aquatic environment unsuitable for many native biota.
There are also several weeds in the Gippsland Lakes Ramsar site that reduce opportunities for regeneration of native flora through competition and changing soil conditions. They include Brazilian milfoil, green macroalgae or ‘broccoli weed’, and Japanese kelp.