Obviously, when wetlands are displaced by farms, houses, or airports, these functions are no longer performed. Although many of the remaining wetlands are protected, others are still being destroyed. This is a particular problem in estuaries because of the intense human activities. In my opinion, introducing a new species to an estuary is nearly always a bad idea. The main problem is that the new species almost has to displace an existing species, the result being that native species become rare and can go extinct.
Nobody knows about such things as phytoplankton or bacteria.
Ballast is taken on in the harbor of origin and kept in ballast tanks while at sea. Then it is discharged in the destination port. The larvae of many marine and estuarine species can survive the trip, and can colonize the new areas. These introductions also occur when fishermen bring in exotic species to try to get them established for their own sport. This has also happened with varous plants introduced for feed, etc.