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. Although aquaculture is often considered an important contribution to feeding growing human populations, marine aquaculture focuses upon luxury markets which maximize profits. Marine aquaculture is often touted as a replacement for fisheries lost to overfishing, but in many cases it may, in fact, negatively impact wild fish populations. For example, in New England money is being requested for developing the aquaculture industry without always considering the impact on the local habitats upon which the recovery of wild fisheries depends.