This book introduces aquaculture ecology as a science of the interaction between commercial aquatic organisms as well as their farming activities and the environment, including the rationales of building and management of aquaculture systems. This book covers productivity and carrying capacity, effects of cyclical fluctuation of environmental factors on aquatic organisms, biological control of water quality, structural optimization of aquaculture systems and ecological prevention of disease. In the last chapter, aquaculture production systems are introduced from multiple perspectives. This book has been designed to provide a stimulating and informative text for researchers in aquaculture, fisheries as well as hydrobiology.