For example, the oyster drill, a species of anemone, and Spartina marsh grass were all accidentally transferred into Pacific coast waters with oysters imported for aquaculture. The use of hatcheries to augment wild populations of popular fisheries species may in the end interfere with those wild populations by interbreeding with them and thereby altering their genetics and survival rates. Aquaculture might also endanger native sealife by exposing it to diseases that run rampant in the overcrowded and stressful conditions of aquaculture facilities. The use of antibiotics to reduce diseases in the culture systems only adds to the potential environmental problems in natural waters. The full effects of antibiotics on native sealife are as yet unknown.
Some coastal aquaculture practices permanency alter natural habitats.
For example, shrimp ponds are often constructed by cutting down mangrove habitats along tropical coastlines. This activity has been responsible for the loss of two-thirds of mangrove forests in the Philippines, more than half in Thailand, and more than a fourth in Ecuador. Aquaculture often uses feed derived from fish caught specifically for fish-meal production. There is, however, a concerted research effort to develop vegetable protein feeds that are efficently utilized. While there are attempts by the aquaculture industry to retrofit some of their technologies to make them individually more sustainable and compatible with the ecosystem, there has been no concerted government or industry effort to evaluate or manage aquaculture to make it regionally sustainable or to integrate it into the ecology and sustainable management of the coastal zone.