Aquaculture for finfish, bivalves, and seaweed is an important and growing food producing sector globally. However, culturing of species in the marine environment implies multiple interactions between farmed species and their environment. This has led to concerns over the ecological effects of aquaculture, which include benthic organic loading, changes to water quality, habitat modification, disease spread, and introduction of exotic or invasive species, interaction with wild species, coastal eutrophication, and marine litter. Over the years, governments and international organizations have recognized the need to identify, mitigate, and reduce these ecological effects. The Food and Agriculture Organization of the United Nations proposes an Ecosystem Approach to Aquaculture (EAA), which implies recognizing its effects at multiple spatial scales, including near-field effect (farm scale) and far-field (bay scale and global scale) effect. This chapter reviews ecological effects of finfish, bivalve, and seaweed aquaculture in marine coastal waters, and describes the mitigation efforts currently used to improve its sustainable management.