Indigenous species are suddenly exposed to new competition for habitats and resources. At worst, the newcomers displace them from their ecological niche. An example is the warty comb jelly (Mnemiopsis leidyi), first found in the Baltic Sea in 2006. Also known as the sea walnut because of its appearance, this jellyfish species preferentially feeds on zooplankton that also provide food for fish larvae, and hence it can indirectly reduce fish stocks. Fish larvae themselves also feature on its menu, however. Non-indigenous species can thus endanger indigenous flora and fauna as predators as well. Fortunately, the kind of extensive harm that this species has been seen to cause in the Black Sea is yet to be observed in the Baltic.

Changes in the gene pool are another potential impact. When indigenous and non-indigenous species interbreed, the result is the loss of genes from the gene pool and hence of biodiversity. The survival of indigenous species or subpopulations, as with salmon, is no longer ensured. An aggravating factor with farmed salmon is that some are genetically engineered and the artificial genes may spread to indigenous stocks.

It is not only the introduced organisms themselves that pose a risk to indigenous flora and fauna. They also bring pathogens and parasites with them. The Chinese mitten crab regularly found as by-catch in North Sea and Baltic Sea since 1915 is an intermediate host of Paragonimus, a flatworm that infests humans and crustacean-eating mammals as a parasite and originally came from Asia.

Non-indigenous species can change the processes and dynamics of an ecosystem so radically that indigenous species are crowded out. As an example, Caulerpa taxifolia, a species of seaweed native to the Indo-Pacific, crowds out seagrass meadows in the Mediterranean, thus altering the entire ecosystem.

Invasive species can even cause economic harm. The mitten crab burrows into banks and coastal defences. The naval shipworm (Teredo navalis), actually a bivalve mollusc rather than a worm, burrows into and destroys timber groynes and other timber structures in the Baltic Sea and has caused damage in the triple-digit millions of euros since 1995. In the case of this particular highly invasive species, however, it is not certain whether it was brought here from elsewhere or if instead it spread from here to the rest of the world.